Starting phenix.real_space_refine on Fri Feb 16 14:29:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/02_2024/6tz2_20587_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 96 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 9573 2.51 5 N 2628 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 15} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "N" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'RNA': 36} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 31} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "T" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 792 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 34} Link IDs: {'rna2p': 2, 'rna3p': 33} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.92, per 1000 atoms: 0.57 Number of scatterers: 15608 At special positions: 0 Unit cell: (119.68, 145.52, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 96 15.00 Mg 2 11.99 O 3255 8.00 N 2628 7.00 C 9573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 13 sheets defined 43.8% alpha, 6.8% beta 21 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 20 through 35 removed outlier: 4.023A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 160 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 201 through 219 Proline residue: A 204 - end of helix removed outlier: 3.509A pdb=" N GLY A 214 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.742A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.756A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.538A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 409 removed outlier: 3.787A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.546A pdb=" N ILE A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.599A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.878A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.838A pdb=" N SER A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.949A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 690 through 706 Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.539A pdb=" N ASP A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 786 Processing helix chain 'A' and resid 801 through 808 Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 869 through 878 removed outlier: 4.381A pdb=" N LEU A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 886 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 902 through 911 Processing helix chain 'A' and resid 927 through 937 Processing helix chain 'A' and resid 946 through 958 Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.504A pdb=" N ALA A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1035 through 1041 removed outlier: 3.951A pdb=" N THR A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1041 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1076 through 1080 Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1104 through 1114 removed outlier: 4.752A pdb=" N ASN A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1132 Processing helix chain 'A' and resid 1155 through 1158 removed outlier: 3.504A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1174 through 1188 removed outlier: 3.627A pdb=" N ASN A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1211 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.517A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.546A pdb=" N LYS B 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.931A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.222A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 360 through 374 removed outlier: 4.324A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.233A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.541A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.937A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.878A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.699A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.767A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 547 through 555 Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.675A pdb=" N TYR A 55 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.852A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 476 through 478 Processing sheet with id= D, first strand: chain 'A' and resid 711 through 716 removed outlier: 3.769A pdb=" N GLU A 714 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 585 through 590 Processing sheet with id= F, first strand: chain 'A' and resid 720 through 722 Processing sheet with id= G, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.682A pdb=" N GLU A1023 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.620A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.450A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.058A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= L, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.598A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 255 through 260 removed outlier: 4.075A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2353 1.30 - 1.43: 4828 1.43 - 1.55: 8648 1.55 - 1.68: 190 1.68 - 1.81: 97 Bond restraints: 16116 Sorted by residual: bond pdb=" C2' ATP A1301 " pdb=" C3' ATP A1301 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C3' UTP A1302 " pdb=" C4' UTP A1302 " ideal model delta sigma weight residual 1.654 1.296 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C2' UTP A1302 " pdb=" C3' UTP A1302 " ideal model delta sigma weight residual 1.301 1.621 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C1' UTP A1302 " pdb=" C2' UTP A1302 " ideal model delta sigma weight residual 1.585 1.326 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C4' UTP A1302 " pdb=" O4' UTP A1302 " ideal model delta sigma weight residual 1.320 1.568 -0.248 2.00e-02 2.50e+03 1.53e+02 ... (remaining 16111 not shown) Histogram of bond angle deviations from ideal: 95.84 - 105.16: 608 105.16 - 114.48: 9727 114.48 - 123.79: 11196 123.79 - 133.11: 692 133.11 - 142.43: 22 Bond angle restraints: 22245 Sorted by residual: angle pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 123.59 142.43 -18.84 1.08e+00 8.64e-01 3.07e+02 angle pdb=" N1 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 118.11 97.49 20.62 1.23e+00 6.64e-01 2.82e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 123.36 13.47 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C1' ATP A1301 " pdb=" N9 ATP A1301 " pdb=" C4 ATP A1301 " ideal model delta sigma weight residual 126.88 108.64 18.24 1.80e+00 3.09e-01 1.03e+02 ... (remaining 22240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 9449 34.55 - 69.10: 251 69.10 - 103.65: 10 103.65 - 138.19: 0 138.19 - 172.74: 1 Dihedral angle restraints: 9711 sinusoidal: 4679 harmonic: 5032 Sorted by residual: dihedral pdb=" O4' U N 19 " pdb=" C1' U N 19 " pdb=" N1 U N 19 " pdb=" C2 U N 19 " ideal model delta sinusoidal sigma weight residual -128.00 44.74 -172.74 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA LYS A 921 " pdb=" C LYS A 921 " pdb=" N LYS A 922 " pdb=" CA LYS A 922 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" O4' U N 20 " pdb=" C1' U N 20 " pdb=" N1 U N 20 " pdb=" C2 U N 20 " ideal model delta sinusoidal sigma weight residual -160.00 -103.19 -56.81 1 1.50e+01 4.44e-03 1.93e+01 ... (remaining 9708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2036 0.060 - 0.121: 453 0.121 - 0.181: 63 0.181 - 0.241: 14 0.241 - 0.301: 4 Chirality restraints: 2570 Sorted by residual: chirality pdb=" CB ILE A 881 " pdb=" CA ILE A 881 " pdb=" CG1 ILE A 881 " pdb=" CG2 ILE A 881 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1' UTP A1302 " pdb=" C2' UTP A1302 " pdb=" N1 UTP A1302 " pdb=" O4' UTP A1302 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 546 " pdb=" CA ILE A 546 " pdb=" CG1 ILE A 546 " pdb=" CG2 ILE A 546 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2567 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.028 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 606 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 996 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C SER A 996 " 0.050 2.00e-02 2.50e+03 pdb=" O SER A 996 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 997 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 538 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.69e+00 pdb=" N PRO B 539 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 539 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 539 " 0.035 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 209 2.64 - 3.20: 13561 3.20 - 3.77: 24380 3.77 - 4.33: 33098 4.33 - 4.90: 52461 Nonbonded interactions: 123709 Sorted by model distance: nonbonded pdb=" O2A UTP A1302 " pdb="MG MG A1303 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1303 " model vdw 2.095 2.170 nonbonded pdb=" O3A UTP A1302 " pdb="MG MG A1304 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASP A 681 " pdb="MG MG A1303 " model vdw 2.112 2.170 nonbonded pdb=" O3G UTP A1302 " pdb="MG MG A1304 " model vdw 2.156 2.170 ... (remaining 123704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 2.610 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 47.530 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.358 16116 Z= 0.574 Angle : 0.951 20.615 22245 Z= 0.546 Chirality : 0.053 0.301 2570 Planarity : 0.007 0.065 2509 Dihedral : 13.602 172.742 6477 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.47 % Allowed : 5.17 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.16), residues: 1701 helix: -2.42 (0.14), residues: 764 sheet: -1.85 (0.39), residues: 150 loop : -2.29 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 606 HIS 0.013 0.002 HIS B 59 PHE 0.034 0.003 PHE A 769 TYR 0.027 0.003 TYR B 286 ARG 0.013 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 513 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 506 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7870 (tp40) cc_final: 0.7644 (mm-40) REVERT: A 374 SER cc_start: 0.8558 (t) cc_final: 0.8292 (p) REVERT: A 415 GLU cc_start: 0.8084 (tp30) cc_final: 0.7580 (tp30) REVERT: A 421 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8103 (tm) REVERT: A 514 ASN cc_start: 0.7599 (t160) cc_final: 0.7011 (p0) REVERT: A 595 ARG cc_start: 0.7392 (ttt90) cc_final: 0.6901 (mmt-90) REVERT: A 630 VAL cc_start: 0.9464 (t) cc_final: 0.9128 (m) REVERT: A 643 ASP cc_start: 0.8541 (p0) cc_final: 0.8027 (p0) REVERT: A 794 LEU cc_start: 0.8339 (tp) cc_final: 0.7958 (tt) REVERT: A 839 MET cc_start: 0.8991 (mmp) cc_final: 0.8709 (mmm) REVERT: A 877 ASP cc_start: 0.8104 (t0) cc_final: 0.7872 (t70) REVERT: A 910 ASP cc_start: 0.8856 (t0) cc_final: 0.8236 (t0) REVERT: A 911 LEU cc_start: 0.9238 (mt) cc_final: 0.8976 (mt) REVERT: A 912 ASN cc_start: 0.8765 (m-40) cc_final: 0.8530 (t0) REVERT: A 942 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8583 (mmtm) REVERT: A 978 GLN cc_start: 0.9230 (tt0) cc_final: 0.9002 (tt0) REVERT: A 1022 TYR cc_start: 0.8341 (p90) cc_final: 0.7666 (p90) REVERT: A 1074 LEU cc_start: 0.8134 (tt) cc_final: 0.7930 (tt) REVERT: B 85 THR cc_start: 0.8954 (m) cc_final: 0.8735 (p) REVERT: B 132 ILE cc_start: 0.9067 (mt) cc_final: 0.8778 (mp) REVERT: B 284 ASP cc_start: 0.8220 (m-30) cc_final: 0.8008 (m-30) REVERT: B 384 ASP cc_start: 0.8806 (p0) cc_final: 0.8576 (p0) REVERT: B 416 SER cc_start: 0.9257 (t) cc_final: 0.8964 (p) REVERT: B 420 GLN cc_start: 0.8145 (mt0) cc_final: 0.7643 (mt0) REVERT: B 433 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 436 GLN cc_start: 0.8507 (mt0) cc_final: 0.8083 (mt0) REVERT: B 464 ASP cc_start: 0.7915 (m-30) cc_final: 0.7619 (m-30) outliers start: 7 outliers final: 2 residues processed: 512 average time/residue: 0.3138 time to fit residues: 227.3725 Evaluate side-chains 324 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 321 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 ASN A 694 HIS A 696 HIS A 820 ASN A 888 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS A1140 HIS ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 180 GLN B 272 ASN B 414 ASN B 542 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16116 Z= 0.230 Angle : 0.561 8.557 22245 Z= 0.288 Chirality : 0.039 0.165 2570 Planarity : 0.005 0.051 2509 Dihedral : 14.296 168.164 3232 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.70 % Allowed : 12.10 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1701 helix: -0.78 (0.17), residues: 775 sheet: -1.61 (0.39), residues: 150 loop : -1.74 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 606 HIS 0.005 0.001 HIS A 694 PHE 0.019 0.001 PHE A 783 TYR 0.030 0.001 TYR A1134 ARG 0.007 0.001 ARG A 882 *********************** 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 389 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 334 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 SER cc_start: 0.8581 (t) cc_final: 0.8368 (p) REVERT: A 415 GLU cc_start: 0.8238 (tp30) cc_final: 0.7689 (tp30) REVERT: A 483 ASP cc_start: 0.8758 (t70) cc_final: 0.8364 (t0) REVERT: A 595 ARG cc_start: 0.7460 (ttt90) cc_final: 0.6956 (mmt-90) REVERT: A 618 THR cc_start: 0.8336 (m) cc_final: 0.8079 (p) REVERT: A 643 ASP cc_start: 0.8514 (p0) cc_final: 0.8044 (p0) REVERT: A 745 GLU cc_start: 0.7071 (tt0) cc_final: 0.6852 (tt0) REVERT: A 794 LEU cc_start: 0.8446 (tp) cc_final: 0.8027 (tt) REVERT: A 844 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 877 ASP cc_start: 0.8178 (t0) cc_final: 0.7927 (t70) REVERT: A 886 GLN cc_start: 0.9003 (tp40) cc_final: 0.8786 (tp40) REVERT: A 910 ASP cc_start: 0.8757 (t0) cc_final: 0.8425 (t0) REVERT: A 971 TYR cc_start: 0.8115 (m-10) cc_final: 0.7738 (m-10) REVERT: A 986 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7756 (pt0) REVERT: A 1130 TYR cc_start: 0.8463 (t80) cc_final: 0.8251 (t80) REVERT: A 1134 TYR cc_start: 0.7878 (p90) cc_final: 0.7536 (p90) REVERT: B 5 ASP cc_start: 0.8203 (t0) cc_final: 0.7980 (t0) REVERT: B 284 ASP cc_start: 0.8064 (m-30) cc_final: 0.7854 (m-30) REVERT: B 359 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7767 (ptpt) REVERT: B 384 ASP cc_start: 0.8787 (p0) cc_final: 0.8517 (p0) REVERT: B 416 SER cc_start: 0.9200 (t) cc_final: 0.8816 (p) REVERT: B 433 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 464 ASP cc_start: 0.7899 (m-30) cc_final: 0.7600 (m-30) outliers start: 55 outliers final: 38 residues processed: 366 average time/residue: 0.3185 time to fit residues: 172.1365 Evaluate side-chains 329 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 180 GLN B 453 ASN B 492 ASN B 542 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16116 Z= 0.271 Angle : 0.545 8.790 22245 Z= 0.279 Chirality : 0.039 0.153 2570 Planarity : 0.004 0.044 2509 Dihedral : 14.206 165.243 3232 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.50 % Allowed : 13.91 % Favored : 81.59 % 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: -1.24 (0.20), residues: 1701 helix: -0.02 (0.18), residues: 776 sheet: -1.40 (0.39), residues: 152 loop : -1.49 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 606 HIS 0.004 0.001 HIS A 696 PHE 0.015 0.001 PHE A 783 TYR 0.025 0.001 TYR A1134 ARG 0.005 0.001 ARG A 744 *********************** 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 362 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASP cc_start: 0.8397 (m-30) cc_final: 0.8179 (t0) REVERT: A 277 GLU cc_start: 0.8186 (tt0) cc_final: 0.7893 (tt0) REVERT: A 374 SER cc_start: 0.8473 (t) cc_final: 0.8257 (p) REVERT: A 415 GLU cc_start: 0.8297 (tp30) cc_final: 0.7756 (tp30) REVERT: A 421 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (tp) REVERT: A 483 ASP cc_start: 0.8648 (t70) cc_final: 0.8107 (t0) REVERT: A 588 GLU cc_start: 0.8427 (tt0) cc_final: 0.8181 (tt0) REVERT: A 595 ARG cc_start: 0.7489 (ttt90) cc_final: 0.6957 (mmt-90) REVERT: A 643 ASP cc_start: 0.8592 (p0) cc_final: 0.8129 (p0) REVERT: A 744 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.8186 (ttp-110) REVERT: A 794 LEU cc_start: 0.8380 (tp) cc_final: 0.7952 (tt) REVERT: A 844 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 854 ASP cc_start: 0.7586 (p0) cc_final: 0.7330 (p0) REVERT: A 877 ASP cc_start: 0.8305 (t0) cc_final: 0.8067 (t70) REVERT: A 886 GLN cc_start: 0.8926 (tp40) cc_final: 0.8704 (tp40) REVERT: A 986 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7720 (pt0) REVERT: A 1191 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8784 (t) REVERT: B 5 ASP cc_start: 0.8286 (t0) cc_final: 0.8071 (t0) REVERT: B 76 MET cc_start: 0.9073 (mtm) cc_final: 0.8791 (mtm) REVERT: B 284 ASP cc_start: 0.8273 (m-30) cc_final: 0.8026 (m-30) REVERT: B 384 ASP cc_start: 0.8796 (p0) cc_final: 0.8527 (p0) REVERT: B 416 SER cc_start: 0.9187 (t) cc_final: 0.8683 (p) outliers start: 67 outliers final: 43 residues processed: 330 average time/residue: 0.3136 time to fit residues: 151.4907 Evaluate side-chains 323 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 278 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 126 HIS A 629 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16116 Z= 0.273 Angle : 0.535 9.050 22245 Z= 0.273 Chirality : 0.039 0.155 2570 Planarity : 0.004 0.040 2509 Dihedral : 14.146 162.316 3232 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.84 % Allowed : 14.52 % Favored : 80.65 % 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: -0.81 (0.20), residues: 1701 helix: 0.42 (0.19), residues: 774 sheet: -1.22 (0.41), residues: 155 loop : -1.35 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 606 HIS 0.005 0.001 HIS B 542 PHE 0.015 0.001 PHE A 783 TYR 0.030 0.001 TYR A1134 ARG 0.005 0.001 ARG A 744 *********************** 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 365 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8465 (ttpp) REVERT: A 277 GLU cc_start: 0.8226 (tt0) cc_final: 0.7932 (tt0) REVERT: A 415 GLU cc_start: 0.8346 (tp30) cc_final: 0.7802 (tp30) REVERT: A 421 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 479 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7397 (tpt170) REVERT: A 483 ASP cc_start: 0.8796 (t70) cc_final: 0.8575 (t70) REVERT: A 595 ARG cc_start: 0.7545 (ttt90) cc_final: 0.7339 (tpp-160) REVERT: A 643 ASP cc_start: 0.8642 (p0) cc_final: 0.8202 (p0) REVERT: A 744 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.8184 (ttp-110) REVERT: A 745 GLU cc_start: 0.6825 (tt0) cc_final: 0.6513 (tt0) REVERT: A 758 MET cc_start: 0.8453 (mmm) cc_final: 0.8041 (mmm) REVERT: A 768 LEU cc_start: 0.9231 (mm) cc_final: 0.9021 (mm) REVERT: A 794 LEU cc_start: 0.8389 (tp) cc_final: 0.8007 (tt) REVERT: A 839 MET cc_start: 0.8867 (mmm) cc_final: 0.8653 (mmm) REVERT: A 844 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 886 GLN cc_start: 0.8927 (tp40) cc_final: 0.8667 (tp-100) REVERT: A 986 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7855 (pt0) REVERT: B 5 ASP cc_start: 0.8288 (t0) cc_final: 0.8068 (t0) REVERT: B 76 MET cc_start: 0.9082 (mtm) cc_final: 0.8796 (mtm) REVERT: B 284 ASP cc_start: 0.8182 (m-30) cc_final: 0.7935 (m-30) REVERT: B 366 TYR cc_start: 0.9200 (t80) cc_final: 0.8731 (t80) REVERT: B 384 ASP cc_start: 0.8809 (p0) cc_final: 0.8485 (p0) REVERT: B 464 ASP cc_start: 0.7984 (m-30) cc_final: 0.7495 (m-30) outliers start: 72 outliers final: 52 residues processed: 332 average time/residue: 0.2897 time to fit residues: 141.0568 Evaluate side-chains 322 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 269 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16116 Z= 0.249 Angle : 0.523 9.126 22245 Z= 0.265 Chirality : 0.039 0.175 2570 Planarity : 0.004 0.040 2509 Dihedral : 14.038 160.887 3232 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.51 % Allowed : 15.12 % Favored : 79.37 % 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: -0.59 (0.20), residues: 1701 helix: 0.59 (0.19), residues: 776 sheet: -1.09 (0.41), residues: 155 loop : -1.22 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 606 HIS 0.005 0.001 HIS B 542 PHE 0.021 0.001 PHE A 175 TYR 0.021 0.001 TYR A1100 ARG 0.004 0.000 ARG A 752 *********************** 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 366 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 284 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8446 (ttpp) REVERT: A 277 GLU cc_start: 0.8229 (tt0) cc_final: 0.7941 (tt0) REVERT: A 415 GLU cc_start: 0.8359 (tp30) cc_final: 0.7853 (tp30) REVERT: A 421 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8756 (tp) REVERT: A 483 ASP cc_start: 0.8789 (t70) cc_final: 0.8508 (t70) REVERT: A 643 ASP cc_start: 0.8658 (p0) cc_final: 0.8232 (p0) REVERT: A 758 MET cc_start: 0.8452 (mmm) cc_final: 0.8247 (mmm) REVERT: A 794 LEU cc_start: 0.8406 (tp) cc_final: 0.8042 (tt) REVERT: A 828 MET cc_start: 0.7549 (ttm) cc_final: 0.7264 (ttm) REVERT: A 886 GLN cc_start: 0.8945 (tp40) cc_final: 0.8680 (tp-100) REVERT: A 959 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8200 (mtp180) REVERT: A 986 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7940 (pt0) REVERT: A 1084 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6808 (t70) REVERT: A 1134 TYR cc_start: 0.7963 (p90) cc_final: 0.7745 (p90) REVERT: A 1191 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8871 (t) REVERT: B 5 ASP cc_start: 0.8280 (t0) cc_final: 0.8049 (t0) REVERT: B 76 MET cc_start: 0.9094 (mtm) cc_final: 0.8791 (mtm) REVERT: B 284 ASP cc_start: 0.8129 (m-30) cc_final: 0.7908 (m-30) REVERT: B 322 MET cc_start: 0.8284 (mtp) cc_final: 0.7951 (mtt) REVERT: B 366 TYR cc_start: 0.9197 (t80) cc_final: 0.8794 (t80) REVERT: B 384 ASP cc_start: 0.8811 (p0) cc_final: 0.8476 (p0) REVERT: B 464 ASP cc_start: 0.7939 (m-30) cc_final: 0.7488 (m-30) outliers start: 82 outliers final: 61 residues processed: 327 average time/residue: 0.2887 time to fit residues: 138.4631 Evaluate side-chains 333 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 269 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 171 optimal weight: 50.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** 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: 0.8507 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16116 Z= 0.319 Angle : 0.564 12.065 22245 Z= 0.287 Chirality : 0.040 0.170 2570 Planarity : 0.004 0.041 2509 Dihedral : 14.038 157.123 3230 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.91 % Allowed : 14.92 % Favored : 79.17 % 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: -0.58 (0.20), residues: 1701 helix: 0.66 (0.19), residues: 769 sheet: -1.10 (0.40), residues: 156 loop : -1.28 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 606 HIS 0.005 0.001 HIS A1036 PHE 0.021 0.002 PHE A 175 TYR 0.014 0.001 TYR A 563 ARG 0.004 0.001 ARG A 303 *********************** 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 348 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 260 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8524 (ttpp) REVERT: A 415 GLU cc_start: 0.8431 (tp30) cc_final: 0.8003 (tp30) REVERT: A 421 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8915 (tp) REVERT: A 483 ASP cc_start: 0.8794 (t70) cc_final: 0.8470 (t70) REVERT: A 617 GLN cc_start: 0.8766 (tp40) cc_final: 0.8398 (mm-40) REVERT: A 643 ASP cc_start: 0.8686 (p0) cc_final: 0.8277 (p0) REVERT: A 841 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7640 (tpt170) REVERT: A 886 GLN cc_start: 0.8974 (tp40) cc_final: 0.8694 (tp-100) REVERT: A 976 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8803 (mtpp) REVERT: A 1084 HIS cc_start: 0.7031 (OUTLIER) cc_final: 0.6773 (t70) REVERT: A 1134 TYR cc_start: 0.8018 (p90) cc_final: 0.7742 (p90) REVERT: A 1191 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8864 (t) REVERT: B 5 ASP cc_start: 0.8291 (t0) cc_final: 0.8066 (t0) REVERT: B 76 MET cc_start: 0.9125 (mtm) cc_final: 0.8835 (mtm) REVERT: B 284 ASP cc_start: 0.8160 (m-30) cc_final: 0.7887 (m-30) REVERT: B 322 MET cc_start: 0.8360 (mtp) cc_final: 0.8026 (mtt) REVERT: B 366 TYR cc_start: 0.9202 (t80) cc_final: 0.8809 (t80) REVERT: B 384 ASP cc_start: 0.8805 (p0) cc_final: 0.8405 (p0) REVERT: B 464 ASP cc_start: 0.7950 (m-30) cc_final: 0.7547 (m-30) outliers start: 88 outliers final: 66 residues processed: 308 average time/residue: 0.2939 time to fit residues: 132.9704 Evaluate side-chains 322 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 252 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 170 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 104 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16116 Z= 0.151 Angle : 0.489 9.822 22245 Z= 0.244 Chirality : 0.038 0.168 2570 Planarity : 0.003 0.042 2509 Dihedral : 13.801 157.733 3230 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.10 % Allowed : 17.27 % Favored : 78.63 % 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: -0.29 (0.21), residues: 1701 helix: 0.90 (0.19), residues: 769 sheet: -0.89 (0.41), residues: 165 loop : -1.12 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.004 0.001 HIS B 542 PHE 0.012 0.001 PHE A 783 TYR 0.023 0.001 TYR A1100 ARG 0.008 0.000 ARG A 744 *********************** 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 359 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 298 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.9112 (m-80) cc_final: 0.8808 (m-80) REVERT: A 415 GLU cc_start: 0.8321 (tp30) cc_final: 0.7906 (tp30) REVERT: A 421 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8871 (tp) REVERT: A 519 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7631 (pp30) REVERT: A 643 ASP cc_start: 0.8693 (p0) cc_final: 0.8287 (p0) REVERT: A 758 MET cc_start: 0.8358 (mmm) cc_final: 0.7792 (mmm) REVERT: A 844 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 1134 TYR cc_start: 0.7953 (p90) cc_final: 0.7567 (p90) REVERT: A 1156 VAL cc_start: 0.9464 (OUTLIER) cc_final: 0.9220 (m) REVERT: A 1191 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8945 (t) REVERT: B 284 ASP cc_start: 0.8057 (m-30) cc_final: 0.7804 (m-30) REVERT: B 322 MET cc_start: 0.8216 (mtp) cc_final: 0.7895 (mtt) REVERT: B 366 TYR cc_start: 0.9214 (t80) cc_final: 0.8816 (t80) REVERT: B 384 ASP cc_start: 0.8774 (p0) cc_final: 0.8380 (p0) REVERT: B 464 ASP cc_start: 0.7848 (m-30) cc_final: 0.7505 (m-30) outliers start: 61 outliers final: 40 residues processed: 327 average time/residue: 0.2889 time to fit residues: 138.8734 Evaluate side-chains 320 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 116 optimal weight: 0.0670 chunk 84 optimal weight: 0.0570 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 3.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS A 480 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16116 Z= 0.172 Angle : 0.508 9.773 22245 Z= 0.253 Chirality : 0.038 0.202 2570 Planarity : 0.003 0.042 2509 Dihedral : 13.741 158.349 3230 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.90 % Allowed : 17.54 % Favored : 78.56 % 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: -0.20 (0.21), residues: 1701 helix: 0.99 (0.19), residues: 770 sheet: -0.97 (0.39), residues: 175 loop : -1.07 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 445 HIS 0.004 0.001 HIS A 999 PHE 0.014 0.001 PHE A 175 TYR 0.023 0.001 TYR A1100 ARG 0.008 0.000 ARG A 744 *********************** 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 343 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.9131 (m-80) cc_final: 0.8770 (m-80) REVERT: A 231 MET cc_start: 0.9010 (mmt) cc_final: 0.8752 (mmt) REVERT: A 415 GLU cc_start: 0.8294 (tp30) cc_final: 0.7896 (tp30) REVERT: A 421 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8875 (tp) REVERT: A 519 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7657 (pp30) REVERT: A 643 ASP cc_start: 0.8680 (p0) cc_final: 0.8287 (p0) REVERT: A 976 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8827 (mtpp) REVERT: A 1134 TYR cc_start: 0.7768 (p90) cc_final: 0.7359 (p90) REVERT: A 1156 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9226 (m) REVERT: A 1191 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8946 (t) REVERT: B 254 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7832 (mp0) REVERT: B 284 ASP cc_start: 0.8071 (m-30) cc_final: 0.7818 (m-30) REVERT: B 322 MET cc_start: 0.8265 (mtp) cc_final: 0.8032 (mtt) REVERT: B 366 TYR cc_start: 0.9200 (t80) cc_final: 0.8856 (t80) REVERT: B 384 ASP cc_start: 0.8776 (p0) cc_final: 0.8408 (p0) REVERT: B 416 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8516 (p) REVERT: B 419 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: B 464 ASP cc_start: 0.7841 (m-30) cc_final: 0.7487 (m-30) outliers start: 58 outliers final: 48 residues processed: 312 average time/residue: 0.2914 time to fit residues: 133.7368 Evaluate side-chains 329 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16116 Z= 0.250 Angle : 0.548 9.391 22245 Z= 0.274 Chirality : 0.040 0.180 2570 Planarity : 0.004 0.043 2509 Dihedral : 13.813 156.976 3230 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.50 % Allowed : 17.20 % Favored : 78.29 % 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: -0.18 (0.21), residues: 1701 helix: 1.01 (0.20), residues: 763 sheet: -0.84 (0.40), residues: 166 loop : -1.09 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 606 HIS 0.004 0.001 HIS B 9 PHE 0.015 0.001 PHE A 175 TYR 0.024 0.001 TYR A1100 ARG 0.003 0.000 ARG A 752 *********************** 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 336 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 269 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8639 (ttpp) REVERT: A 160 TYR cc_start: 0.9150 (m-80) cc_final: 0.8851 (m-80) REVERT: A 231 MET cc_start: 0.8959 (mmt) cc_final: 0.8627 (mmt) REVERT: A 415 GLU cc_start: 0.8325 (tp30) cc_final: 0.8015 (tp30) REVERT: A 421 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8894 (tp) REVERT: A 643 ASP cc_start: 0.8680 (p0) cc_final: 0.8277 (p0) REVERT: A 844 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 976 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (mtpp) REVERT: A 1134 TYR cc_start: 0.7904 (p90) cc_final: 0.7510 (p90) REVERT: A 1156 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9216 (m) REVERT: A 1191 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8944 (t) REVERT: B 284 ASP cc_start: 0.8066 (m-30) cc_final: 0.7777 (m-30) REVERT: B 366 TYR cc_start: 0.9205 (t80) cc_final: 0.8888 (t80) REVERT: B 384 ASP cc_start: 0.8785 (p0) cc_final: 0.8393 (p0) REVERT: B 419 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: B 443 ARG cc_start: 0.6475 (mtt180) cc_final: 0.6190 (mtt180) REVERT: B 464 ASP cc_start: 0.7893 (m-30) cc_final: 0.7523 (m-30) outliers start: 67 outliers final: 53 residues processed: 306 average time/residue: 0.2853 time to fit residues: 129.1176 Evaluate side-chains 324 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 116 optimal weight: 0.0000 chunk 176 optimal weight: 50.0000 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16116 Z= 0.221 Angle : 0.539 9.770 22245 Z= 0.268 Chirality : 0.039 0.182 2570 Planarity : 0.004 0.045 2509 Dihedral : 13.798 155.930 3230 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.30 % Allowed : 17.67 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1701 helix: 1.02 (0.20), residues: 762 sheet: -0.82 (0.40), residues: 166 loop : -1.06 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 187 HIS 0.004 0.001 HIS A 999 PHE 0.014 0.001 PHE A 175 TYR 0.016 0.001 TYR A1100 ARG 0.003 0.000 ARG A 752 ********************** 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 331 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 267 time to evaluate : 1.902 Fit side-chains REVERT: A 116 TYR cc_start: 0.8727 (m-80) cc_final: 0.8222 (m-80) REVERT: A 131 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8592 (ttpp) REVERT: A 160 TYR cc_start: 0.9159 (m-80) cc_final: 0.8863 (m-80) REVERT: A 231 MET cc_start: 0.8947 (mmt) cc_final: 0.8638 (mmt) REVERT: A 415 GLU cc_start: 0.8314 (tp30) cc_final: 0.8022 (tp30) REVERT: A 421 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (tp) REVERT: A 643 ASP cc_start: 0.8673 (p0) cc_final: 0.8268 (p0) REVERT: A 844 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 942 LYS cc_start: 0.9091 (mmpt) cc_final: 0.8655 (tppt) REVERT: A 976 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8776 (mtpp) REVERT: A 1134 TYR cc_start: 0.7914 (p90) cc_final: 0.7548 (p90) REVERT: A 1156 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9215 (m) REVERT: A 1191 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8945 (t) REVERT: B 284 ASP cc_start: 0.8045 (m-30) cc_final: 0.7763 (m-30) REVERT: B 366 TYR cc_start: 0.9205 (t80) cc_final: 0.8827 (t80) REVERT: B 384 ASP cc_start: 0.8770 (p0) cc_final: 0.8399 (p0) REVERT: B 416 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 419 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: B 464 ASP cc_start: 0.7869 (m-30) cc_final: 0.7502 (m-30) outliers start: 64 outliers final: 54 residues processed: 301 average time/residue: 0.3008 time to fit residues: 134.1760 Evaluate side-chains 325 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 965 ASN Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098295 restraints weight = 27779.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100625 restraints weight = 13884.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102138 restraints weight = 8998.719| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16116 Z= 0.289 Angle : 0.571 10.046 22245 Z= 0.286 Chirality : 0.040 0.181 2570 Planarity : 0.004 0.045 2509 Dihedral : 13.862 153.614 3230 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.57 % Allowed : 17.47 % Favored : 77.96 % 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: -0.19 (0.21), residues: 1701 helix: 0.98 (0.20), residues: 761 sheet: -0.90 (0.39), residues: 167 loop : -1.04 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.005 0.001 HIS B 9 PHE 0.016 0.001 PHE A 175 TYR 0.020 0.001 TYR A1100 ARG 0.004 0.000 ARG A 752 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.24 seconds wall clock time: 62 minutes 14.36 seconds (3734.36 seconds total)