Starting phenix.real_space_refine on Thu Mar 5 23:53:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btp_30181/03_2026/7btp_30181.map" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7905 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 12997 2.51 5 N 3388 2.21 5 O 3939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20371 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "A" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 957} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3739 Classifications: {'peptide': 473} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Restraints were copied for chains: C, F Time building chain proxies: 4.96, per 1000 atoms: 0.24 Number of scatterers: 20371 At special positions: 0 Unit cell: (137.7, 149.85, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 3939 8.00 N 3388 7.00 C 12997 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 - 3.00 Amino acid : True - 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: 1.50 Conformation dependent library (CDL) restraints added in 943.7 milliseconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4850 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 48.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'E' and resid 111 through 119 removed outlier: 4.136A pdb=" N ASN E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 157 through 193 removed outlier: 4.390A pdb=" N ILE E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 193 " --> pdb=" O TYR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.890A pdb=" N VAL E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 354 through 369 Processing helix chain 'E' and resid 374 through 394 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.547A pdb=" N ALA A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.340A pdb=" N THR A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.571A pdb=" N TYR A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.554A pdb=" N TYR A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 removed outlier: 3.628A pdb=" N GLN A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.548A pdb=" N ALA A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.546A pdb=" N THR A 491 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 492 " --> pdb=" O LEU A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 509 through 528 removed outlier: 5.727A pdb=" N ARG A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 569 removed outlier: 3.972A pdb=" N ALA A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.975A pdb=" N MET A 604 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 624 removed outlier: 3.693A pdb=" N LYS A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 4.000A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.601A pdb=" N GLN A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.832A pdb=" N LEU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.613A pdb=" N LEU A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.557A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 793 removed outlier: 4.119A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 811 through 823 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.541A pdb=" N LYS A 915 " --> pdb=" O ILE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 926 through 936 removed outlier: 4.083A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 Processing helix chain 'A' and resid 945 through 971 removed outlier: 3.886A pdb=" N ILE A 949 " --> pdb=" O ASP A 945 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 990 Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 3.866A pdb=" N GLN A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.556A pdb=" N VAL B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 55 removed outlier: 3.651A pdb=" N PHE B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN B 34 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.505A pdb=" N SER B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.991A pdb=" N SER B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.610A pdb=" N SER B 125 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.547A pdb=" N GLU B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.228A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.612A pdb=" N ASN B 261 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.786A pdb=" N PHE B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.686A pdb=" N GLU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 removed outlier: 4.145A pdb=" N SER B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.866A pdb=" N LEU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.556A pdb=" N VAL C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 55 removed outlier: 3.651A pdb=" N PHE C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN C 34 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.506A pdb=" N SER C 89 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.991A pdb=" N SER C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.611A pdb=" N SER C 125 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 164 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 186 removed outlier: 3.548A pdb=" N GLU C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.228A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.612A pdb=" N ASN C 261 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.787A pdb=" N PHE C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.687A pdb=" N GLU C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 378 " --> pdb=" O TYR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 445 removed outlier: 4.145A pdb=" N SER C 445 " --> pdb=" O GLN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.866A pdb=" N LEU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 499 " --> pdb=" O THR C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.845A pdb=" N VAL D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 4.048A pdb=" N ASP D 42 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 101 Processing helix chain 'F' and resid 6 through 26 removed outlier: 3.845A pdb=" N VAL F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 45 removed outlier: 4.047A pdb=" N ASP F 42 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN F 43 " --> pdb=" O MET F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 76 through 101 Processing sheet with id=AA1, first strand: chain 'E' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'E' and resid 26 through 28 removed outlier: 3.650A pdb=" N LYS E 99 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 202 through 205 removed outlier: 3.843A pdb=" N GLU E 202 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 249 through 251 removed outlier: 4.621A pdb=" N ASP E 249 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 284 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.328A pdb=" N GLU A 50 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLN A 138 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 152 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 154 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.937A pdb=" N ARG A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 264 removed outlier: 4.141A pdb=" N THR A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.537A pdb=" N LYS A 332 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE A 406 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 334 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A 304 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A 460 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP A 306 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 479 removed outlier: 7.079A pdb=" N LYS A 474 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A 702 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 476 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 704 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP A 478 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 669 " --> pdb=" O ASN A 701 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 703 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 671 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 539 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 670 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA A 540 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL A 655 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 542 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA A 577 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 741 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 300 removed outlier: 6.392A pdb=" N PHE B 296 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS B 350 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 298 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 352 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL B 300 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 354 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 381 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 413 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 384 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 300 removed outlier: 6.391A pdb=" N PHE C 296 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS C 350 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 298 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 352 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 300 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 354 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER C 405 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 381 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 413 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 384 " --> pdb=" O VAL C 413 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6565 1.34 - 1.46: 4291 1.46 - 1.58: 9839 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 20780 Sorted by residual: bond pdb=" C LEU E 121 " pdb=" N PRO E 122 " ideal model delta sigma weight residual 1.332 1.351 -0.019 8.20e-03 1.49e+04 5.27e+00 bond pdb=" CA ARG B 142 " pdb=" C ARG B 142 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.18e-02 7.18e+03 4.50e+00 bond pdb=" CA ARG C 142 " pdb=" C ARG C 142 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.18e-02 7.18e+03 4.10e+00 bond pdb=" C THR C 409 " pdb=" N ASP C 410 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C THR B 409 " pdb=" N ASP B 410 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.70e+00 ... (remaining 20775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 27405 3.01 - 6.02: 588 6.02 - 9.03: 94 9.03 - 12.04: 17 12.04 - 15.05: 2 Bond angle restraints: 28106 Sorted by residual: angle pdb=" C THR B 395 " pdb=" N THR B 396 " pdb=" CA THR B 396 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C THR C 395 " pdb=" N THR C 396 " pdb=" CA THR C 396 " ideal model delta sigma weight residual 121.70 132.34 -10.64 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C THR C 409 " pdb=" N ASP C 410 " pdb=" CA ASP C 410 " ideal model delta sigma weight residual 121.70 132.11 -10.41 1.80e+00 3.09e-01 3.34e+01 angle pdb=" C THR B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.70 132.07 -10.37 1.80e+00 3.09e-01 3.32e+01 angle pdb=" C THR A 26 " pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta sigma weight residual 121.70 131.59 -9.89 1.80e+00 3.09e-01 3.02e+01 ... (remaining 28101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 11520 15.75 - 31.51: 777 31.51 - 47.26: 168 47.26 - 63.01: 6 63.01 - 78.76: 18 Dihedral angle restraints: 12489 sinusoidal: 5010 harmonic: 7479 Sorted by residual: dihedral pdb=" CA ARG A 678 " pdb=" C ARG A 678 " pdb=" N TYR A 679 " pdb=" CA TYR A 679 " ideal model delta harmonic sigma weight residual 180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA VAL B 474 " pdb=" C VAL B 474 " pdb=" N GLU B 475 " pdb=" CA GLU B 475 " ideal model delta harmonic sigma weight residual 180.00 133.68 46.32 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA VAL C 474 " pdb=" C VAL C 474 " pdb=" N GLU C 475 " pdb=" CA GLU C 475 " ideal model delta harmonic sigma weight residual 180.00 133.75 46.25 0 5.00e+00 4.00e-02 8.56e+01 ... (remaining 12486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2399 0.069 - 0.138: 629 0.138 - 0.206: 66 0.206 - 0.275: 15 0.275 - 0.344: 5 Chirality restraints: 3114 Sorted by residual: chirality pdb=" CB ILE A 378 " pdb=" CA ILE A 378 " pdb=" CG1 ILE A 378 " pdb=" CG2 ILE A 378 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE B 79 " pdb=" CA ILE B 79 " pdb=" CG1 ILE B 79 " pdb=" CG2 ILE B 79 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE C 79 " pdb=" CA ILE C 79 " pdb=" CG1 ILE C 79 " pdb=" CG2 ILE C 79 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3111 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 72 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO E 73 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 73 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 73 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1007 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A1008 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A1008 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1008 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 765 " -0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 766 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 766 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 766 " -0.040 5.00e-02 4.00e+02 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3179 2.76 - 3.29: 19815 3.29 - 3.83: 33595 3.83 - 4.36: 38405 4.36 - 4.90: 62850 Nonbonded interactions: 157844 Sorted by model distance: nonbonded pdb=" OH TYR F 7 " pdb=" OD2 ASP F 92 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR D 7 " pdb=" OD2 ASP D 92 " model vdw 2.222 3.040 nonbonded pdb=" O ALA E 255 " pdb=" OG SER E 259 " model vdw 2.265 3.040 nonbonded pdb=" O PRO A1008 " pdb=" OH TYR C 84 " model vdw 2.266 3.040 nonbonded pdb=" O LEU A 342 " pdb=" OG1 THR A 346 " model vdw 2.272 3.040 ... (remaining 157839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.007 0.076 20780 Z= 0.333 Angle : 1.118 15.047 28106 Z= 0.608 Chirality : 0.061 0.344 3114 Planarity : 0.007 0.101 3646 Dihedral : 11.602 78.762 7639 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.63 % Favored : 88.33 % Rotamer: Outliers : 0.59 % Allowed : 5.33 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.13), residues: 2502 helix: -2.31 (0.12), residues: 1077 sheet: -2.73 (0.28), residues: 238 loop : -3.68 (0.14), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 841 TYR 0.039 0.003 TYR C 260 PHE 0.026 0.003 PHE A 599 TRP 0.053 0.004 TRP E 117 HIS 0.011 0.003 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00700 (20780) covalent geometry : angle 1.11843 (28106) hydrogen bonds : bond 0.16611 ( 825) hydrogen bonds : angle 7.15437 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 373 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 THR cc_start: 0.5013 (m) cc_final: 0.4507 (m) REVERT: A 212 PHE cc_start: 0.7129 (m-80) cc_final: 0.6856 (m-80) REVERT: A 252 THR cc_start: 0.9145 (m) cc_final: 0.8722 (t) REVERT: A 315 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 589 ASN cc_start: 0.6636 (p0) cc_final: 0.5411 (p0) REVERT: A 701 ASN cc_start: 0.8362 (m-40) cc_final: 0.8099 (m110) REVERT: B 262 LEU cc_start: 0.9214 (pp) cc_final: 0.8884 (pp) REVERT: B 436 ILE cc_start: 0.8434 (pp) cc_final: 0.8193 (pt) REVERT: B 440 MET cc_start: 0.7997 (tpt) cc_final: 0.7755 (tpt) REVERT: C 201 THR cc_start: 0.7087 (m) cc_final: 0.6699 (p) REVERT: C 223 ILE cc_start: 0.9213 (tt) cc_final: 0.9005 (mt) REVERT: C 275 ASP cc_start: 0.7306 (p0) cc_final: 0.7101 (p0) REVERT: C 276 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7100 (mtmm) REVERT: D 15 TYR cc_start: 0.8056 (t80) cc_final: 0.7638 (t80) REVERT: D 48 TYR cc_start: 0.6981 (m-80) cc_final: 0.6686 (m-80) REVERT: D 79 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8411 (mmm-85) REVERT: F 89 LEU cc_start: 0.9388 (mt) cc_final: 0.8753 (pp) outliers start: 13 outliers final: 1 residues processed: 384 average time/residue: 0.1620 time to fit residues: 90.8521 Evaluate side-chains 166 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 247 optimal weight: 0.0470 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS A 419 GLN A 522 ASN A 588 GLN A 635 GLN B 219 HIS B 373 GLN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 373 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN C 479 ASN D 13 HIS D 88 GLN F 13 HIS F 43 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.083665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061717 restraints weight = 112366.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.063337 restraints weight = 65482.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.064408 restraints weight = 46267.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.065102 restraints weight = 36895.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.065545 restraints weight = 31876.623| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20780 Z= 0.133 Angle : 0.693 8.835 28106 Z= 0.370 Chirality : 0.046 0.211 3114 Planarity : 0.005 0.085 3646 Dihedral : 6.761 37.283 2730 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.09 % Allowed : 2.87 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.15), residues: 2502 helix: -0.80 (0.14), residues: 1119 sheet: -2.34 (0.29), residues: 258 loop : -3.44 (0.15), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 503 TYR 0.018 0.001 TYR C 260 PHE 0.017 0.001 PHE C 41 TRP 0.051 0.002 TRP E 117 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00271 (20780) covalent geometry : angle 0.69302 (28106) hydrogen bonds : bond 0.03987 ( 825) hydrogen bonds : angle 5.15102 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 MET cc_start: 0.9114 (ptm) cc_final: 0.8808 (ptm) REVERT: E 314 MET cc_start: 0.7822 (tpt) cc_final: 0.7370 (mmm) REVERT: E 328 LYS cc_start: 0.5353 (tttp) cc_final: 0.4965 (ttpt) REVERT: A 252 THR cc_start: 0.9274 (m) cc_final: 0.8917 (t) REVERT: A 589 ASN cc_start: 0.6584 (p0) cc_final: 0.5900 (p0) REVERT: A 910 MET cc_start: 0.7701 (mmp) cc_final: 0.6716 (mmp) REVERT: B 136 PHE cc_start: 0.8137 (t80) cc_final: 0.7402 (t80) REVERT: B 239 LYS cc_start: 0.8083 (tptm) cc_final: 0.7855 (ptmt) REVERT: C 37 LEU cc_start: 0.9464 (mt) cc_final: 0.9237 (mp) REVERT: C 181 TYR cc_start: 0.7662 (t80) cc_final: 0.7462 (t80) REVERT: C 223 ILE cc_start: 0.9104 (tt) cc_final: 0.8706 (mp) REVERT: C 276 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7745 (ttmt) REVERT: C 281 LEU cc_start: 0.9150 (tp) cc_final: 0.8885 (tp) REVERT: C 377 ASP cc_start: 0.8945 (t0) cc_final: 0.8572 (t70) REVERT: C 440 MET cc_start: 0.8397 (tpt) cc_final: 0.8123 (tpp) REVERT: D 12 ASP cc_start: 0.9184 (m-30) cc_final: 0.8973 (m-30) REVERT: D 17 MET cc_start: 0.8362 (ttm) cc_final: 0.8118 (ttm) REVERT: D 48 TYR cc_start: 0.6575 (m-80) cc_final: 0.5949 (m-80) REVERT: D 55 VAL cc_start: 0.8763 (p) cc_final: 0.8512 (m) REVERT: D 79 ARG cc_start: 0.9237 (mmt90) cc_final: 0.8703 (mmm-85) REVERT: F 8 ASN cc_start: 0.9608 (m-40) cc_final: 0.9197 (t0) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.1414 time to fit residues: 52.4253 Evaluate side-chains 148 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 129 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 69 GLN A 91 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN B 21 ASN B 211 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 102 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.076821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055033 restraints weight = 112599.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.056451 restraints weight = 66545.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057373 restraints weight = 47777.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057944 restraints weight = 38643.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058345 restraints weight = 33777.366| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20780 Z= 0.313 Angle : 0.859 12.963 28106 Z= 0.458 Chirality : 0.049 0.244 3114 Planarity : 0.006 0.072 3646 Dihedral : 7.010 41.314 2730 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2502 helix: -0.38 (0.15), residues: 1137 sheet: -2.47 (0.30), residues: 243 loop : -3.26 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 352 TYR 0.029 0.002 TYR A 795 PHE 0.027 0.003 PHE B 277 TRP 0.073 0.003 TRP E 117 HIS 0.007 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00666 (20780) covalent geometry : angle 0.85931 (28106) hydrogen bonds : bond 0.04813 ( 825) hydrogen bonds : angle 5.33972 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 117 TRP cc_start: 0.7688 (m-90) cc_final: 0.7476 (m-90) REVERT: E 203 TRP cc_start: 0.8192 (m-10) cc_final: 0.7839 (m100) REVERT: E 314 MET cc_start: 0.7965 (tpt) cc_final: 0.7497 (mmm) REVERT: A 130 MET cc_start: 0.8620 (mmt) cc_final: 0.8156 (mmt) REVERT: A 254 LEU cc_start: 0.9402 (tt) cc_final: 0.9024 (mt) REVERT: A 309 THR cc_start: 0.7822 (m) cc_final: 0.7501 (t) REVERT: A 390 MET cc_start: 0.9021 (ttm) cc_final: 0.8761 (ttm) REVERT: A 511 MET cc_start: 0.7998 (tpt) cc_final: 0.7791 (tpp) REVERT: A 683 MET cc_start: 0.7997 (ptt) cc_final: 0.7723 (ptt) REVERT: A 994 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7740 (tt0) REVERT: B 82 LYS cc_start: 0.8265 (tptt) cc_final: 0.7770 (tmtt) REVERT: B 141 ASN cc_start: 0.8128 (t0) cc_final: 0.7696 (t0) REVERT: B 254 GLU cc_start: 0.8180 (tp30) cc_final: 0.7772 (tm-30) REVERT: C 223 ILE cc_start: 0.9319 (tt) cc_final: 0.9062 (mt) REVERT: C 377 ASP cc_start: 0.9115 (t0) cc_final: 0.8754 (t70) REVERT: C 387 LEU cc_start: 0.9133 (tp) cc_final: 0.8931 (tt) REVERT: C 440 MET cc_start: 0.9029 (tpt) cc_final: 0.8777 (tpp) REVERT: D 17 MET cc_start: 0.8328 (ttm) cc_final: 0.8116 (ttm) REVERT: D 48 TYR cc_start: 0.7771 (m-80) cc_final: 0.7528 (m-80) REVERT: D 55 VAL cc_start: 0.9052 (p) cc_final: 0.8788 (m) REVERT: D 79 ARG cc_start: 0.9249 (mmt90) cc_final: 0.8896 (mmt180) REVERT: D 86 TYR cc_start: 0.9345 (t80) cc_final: 0.9124 (t80) REVERT: F 82 GLN cc_start: 0.9433 (mt0) cc_final: 0.9207 (mp10) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.1329 time to fit residues: 34.4836 Evaluate side-chains 103 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 152 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.079501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057576 restraints weight = 111326.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059109 restraints weight = 64324.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060122 restraints weight = 45422.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060746 restraints weight = 36332.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.061191 restraints weight = 31518.603| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20780 Z= 0.127 Angle : 0.666 9.381 28106 Z= 0.353 Chirality : 0.045 0.231 3114 Planarity : 0.005 0.091 3646 Dihedral : 6.220 35.351 2730 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.14 % Allowed : 2.91 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2502 helix: 0.28 (0.16), residues: 1121 sheet: -2.31 (0.30), residues: 263 loop : -2.94 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 322 TYR 0.021 0.001 TYR A 30 PHE 0.023 0.001 PHE C 92 TRP 0.039 0.002 TRP C 17 HIS 0.006 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00268 (20780) covalent geometry : angle 0.66619 (28106) hydrogen bonds : bond 0.03592 ( 825) hydrogen bonds : angle 4.72849 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 MET cc_start: 0.2032 (mmp) cc_final: 0.1668 (tpp) REVERT: E 314 MET cc_start: 0.7850 (tpt) cc_final: 0.7382 (mmm) REVERT: A 130 MET cc_start: 0.8589 (mmt) cc_final: 0.8077 (mmt) REVERT: A 344 TYR cc_start: 0.8782 (t80) cc_final: 0.8233 (t80) REVERT: A 350 TYR cc_start: 0.8035 (m-10) cc_final: 0.7703 (m-10) REVERT: A 390 MET cc_start: 0.9008 (ttm) cc_final: 0.8726 (ttm) REVERT: A 589 ASN cc_start: 0.6377 (p0) cc_final: 0.5564 (p0) REVERT: A 683 MET cc_start: 0.7758 (ptt) cc_final: 0.7414 (ptt) REVERT: B 82 LYS cc_start: 0.8186 (tptt) cc_final: 0.7739 (tmtt) REVERT: C 223 ILE cc_start: 0.8850 (tt) cc_final: 0.8642 (mp) REVERT: D 55 VAL cc_start: 0.9115 (p) cc_final: 0.8841 (m) REVERT: D 79 ARG cc_start: 0.9208 (mmt90) cc_final: 0.8660 (mmm-85) REVERT: D 88 GLN cc_start: 0.9381 (tp40) cc_final: 0.8721 (tp-100) outliers start: 3 outliers final: 0 residues processed: 172 average time/residue: 0.1334 time to fit residues: 36.7466 Evaluate side-chains 101 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 244 HIS B 289 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 102 ASN C 373 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056227 restraints weight = 112513.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057720 restraints weight = 65923.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058705 restraints weight = 47135.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059290 restraints weight = 38054.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059725 restraints weight = 33291.049| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20780 Z= 0.160 Angle : 0.673 8.353 28106 Z= 0.356 Chirality : 0.045 0.281 3114 Planarity : 0.005 0.072 3646 Dihedral : 6.048 34.667 2730 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2502 helix: 0.42 (0.16), residues: 1147 sheet: -2.28 (0.30), residues: 271 loop : -2.86 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 14 TYR 0.022 0.001 TYR B 346 PHE 0.032 0.002 PHE B 277 TRP 0.034 0.002 TRP C 17 HIS 0.006 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00342 (20780) covalent geometry : angle 0.67326 (28106) hydrogen bonds : bond 0.03595 ( 825) hydrogen bonds : angle 4.64594 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 117 TRP cc_start: 0.7474 (m-10) cc_final: 0.7232 (m-10) REVERT: E 181 MET cc_start: 0.9047 (ptm) cc_final: 0.8814 (ptm) REVERT: E 314 MET cc_start: 0.7853 (tpt) cc_final: 0.7418 (mmm) REVERT: A 130 MET cc_start: 0.8644 (mmt) cc_final: 0.8186 (mmt) REVERT: A 227 MET cc_start: 0.8731 (mpp) cc_final: 0.8079 (mpp) REVERT: A 344 TYR cc_start: 0.8875 (t80) cc_final: 0.8234 (t80) REVERT: A 390 MET cc_start: 0.9026 (ttm) cc_final: 0.8813 (ttm) REVERT: A 604 MET cc_start: 0.7830 (pmm) cc_final: 0.7623 (pmm) REVERT: A 683 MET cc_start: 0.7853 (ptt) cc_final: 0.7547 (ptt) REVERT: A 994 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7541 (tt0) REVERT: B 82 LYS cc_start: 0.8319 (tptt) cc_final: 0.7733 (tmtt) REVERT: B 440 MET cc_start: 0.8814 (tpt) cc_final: 0.8541 (tmm) REVERT: C 223 ILE cc_start: 0.9190 (tt) cc_final: 0.8909 (mp) REVERT: D 55 VAL cc_start: 0.9224 (p) cc_final: 0.8948 (m) REVERT: D 79 ARG cc_start: 0.9295 (mmt90) cc_final: 0.8662 (mmm-85) REVERT: D 81 LEU cc_start: 0.9445 (mt) cc_final: 0.9228 (pp) REVERT: F 78 ILE cc_start: 0.9594 (pt) cc_final: 0.9378 (mm) REVERT: F 89 LEU cc_start: 0.9454 (mm) cc_final: 0.9220 (mm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1260 time to fit residues: 31.1825 Evaluate side-chains 98 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 526 GLN B 345 ASN B 373 GLN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 217 GLN C 244 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.075655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054283 restraints weight = 112884.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.056118 restraints weight = 72456.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056437 restraints weight = 45415.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056638 restraints weight = 38543.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056719 restraints weight = 36122.454| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 20780 Z= 0.275 Angle : 0.778 8.723 28106 Z= 0.415 Chirality : 0.048 0.212 3114 Planarity : 0.005 0.058 3646 Dihedral : 6.496 36.320 2730 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2502 helix: 0.16 (0.15), residues: 1163 sheet: -2.31 (0.31), residues: 256 loop : -3.00 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 153 TYR 0.018 0.002 TYR B 466 PHE 0.058 0.002 PHE B 277 TRP 0.048 0.002 TRP C 17 HIS 0.008 0.002 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00588 (20780) covalent geometry : angle 0.77836 (28106) hydrogen bonds : bond 0.04097 ( 825) hydrogen bonds : angle 4.96903 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 TRP cc_start: 0.8142 (m-10) cc_final: 0.7739 (m100) REVERT: E 239 MET cc_start: 0.2492 (mmp) cc_final: 0.2130 (tpp) REVERT: E 314 MET cc_start: 0.7861 (tpt) cc_final: 0.7544 (mmm) REVERT: A 130 MET cc_start: 0.8613 (mmt) cc_final: 0.8238 (mmt) REVERT: A 227 MET cc_start: 0.8947 (mpp) cc_final: 0.8322 (mpp) REVERT: A 309 THR cc_start: 0.8031 (m) cc_final: 0.7759 (t) REVERT: A 390 MET cc_start: 0.8947 (ttm) cc_final: 0.8742 (ttm) REVERT: A 511 MET cc_start: 0.8023 (tpt) cc_final: 0.7804 (tpt) REVERT: A 683 MET cc_start: 0.7975 (ptt) cc_final: 0.7673 (ptt) REVERT: A 994 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7607 (tt0) REVERT: B 181 TYR cc_start: 0.8952 (t80) cc_final: 0.8577 (t80) REVERT: C 136 PHE cc_start: 0.7600 (p90) cc_final: 0.6896 (p90) REVERT: C 223 ILE cc_start: 0.9194 (tt) cc_final: 0.8880 (mp) REVERT: D 79 ARG cc_start: 0.9303 (mmt90) cc_final: 0.8760 (mmm-85) REVERT: F 6 THR cc_start: 0.8955 (t) cc_final: 0.8733 (t) REVERT: F 15 TYR cc_start: 0.8573 (t80) cc_final: 0.8232 (t80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1237 time to fit residues: 28.9304 Evaluate side-chains 102 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 9 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 188 optimal weight: 0.0040 chunk 203 optimal weight: 0.9990 chunk 138 optimal weight: 0.0060 chunk 114 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.056436 restraints weight = 111050.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.058235 restraints weight = 68531.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058806 restraints weight = 41815.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.058928 restraints weight = 36056.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059023 restraints weight = 33810.244| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20780 Z= 0.130 Angle : 0.665 8.897 28106 Z= 0.348 Chirality : 0.045 0.193 3114 Planarity : 0.004 0.058 3646 Dihedral : 5.931 32.706 2730 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2502 helix: 0.53 (0.16), residues: 1151 sheet: -2.27 (0.30), residues: 273 loop : -2.79 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.017 0.001 TYR B 181 PHE 0.040 0.001 PHE B 277 TRP 0.034 0.002 TRP C 17 HIS 0.006 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00279 (20780) covalent geometry : angle 0.66459 (28106) hydrogen bonds : bond 0.03448 ( 825) hydrogen bonds : angle 4.58004 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 MET cc_start: 0.9074 (ptm) cc_final: 0.8795 (ppp) REVERT: E 203 TRP cc_start: 0.7948 (m-10) cc_final: 0.7580 (m100) REVERT: E 239 MET cc_start: 0.1764 (mmp) cc_final: 0.1513 (tpp) REVERT: E 314 MET cc_start: 0.8101 (tpt) cc_final: 0.7891 (mmm) REVERT: A 227 MET cc_start: 0.8929 (mpp) cc_final: 0.8016 (mpp) REVERT: A 390 MET cc_start: 0.8935 (ttm) cc_final: 0.8647 (ttp) REVERT: A 511 MET cc_start: 0.7923 (tpt) cc_final: 0.7646 (tpp) REVERT: A 589 ASN cc_start: 0.6735 (p0) cc_final: 0.6524 (p0) REVERT: A 604 MET cc_start: 0.7922 (pmm) cc_final: 0.7532 (pmm) REVERT: A 683 MET cc_start: 0.7877 (ptt) cc_final: 0.7599 (ptt) REVERT: B 181 TYR cc_start: 0.8925 (t80) cc_final: 0.8501 (t80) REVERT: B 265 MET cc_start: 0.9078 (ttm) cc_final: 0.8687 (mmm) REVERT: B 290 PHE cc_start: 0.6898 (m-80) cc_final: 0.6646 (m-80) REVERT: C 136 PHE cc_start: 0.7656 (p90) cc_final: 0.6998 (p90) REVERT: C 223 ILE cc_start: 0.9072 (tt) cc_final: 0.8857 (mp) REVERT: C 265 MET cc_start: 0.9419 (mtm) cc_final: 0.8935 (mtt) REVERT: D 70 LEU cc_start: 0.8275 (mm) cc_final: 0.8011 (mm) REVERT: D 79 ARG cc_start: 0.9304 (mmt90) cc_final: 0.8826 (mmm-85) REVERT: D 88 GLN cc_start: 0.9461 (tp40) cc_final: 0.8702 (tp-100) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1129 time to fit residues: 26.2235 Evaluate side-chains 96 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 193 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 102 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.076875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055567 restraints weight = 113343.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057145 restraints weight = 68806.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057498 restraints weight = 44471.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057790 restraints weight = 37202.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057791 restraints weight = 35002.677| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20780 Z= 0.184 Angle : 0.699 8.235 28106 Z= 0.368 Chirality : 0.046 0.279 3114 Planarity : 0.005 0.059 3646 Dihedral : 6.006 32.630 2730 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2502 helix: 0.51 (0.16), residues: 1159 sheet: -2.02 (0.31), residues: 261 loop : -2.86 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 132 TYR 0.031 0.002 TYR F 15 PHE 0.040 0.002 PHE B 277 TRP 0.088 0.002 TRP E 117 HIS 0.007 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00395 (20780) covalent geometry : angle 0.69945 (28106) hydrogen bonds : bond 0.03622 ( 825) hydrogen bonds : angle 4.65912 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 MET cc_start: 0.9160 (ptm) cc_final: 0.8701 (ppp) REVERT: E 239 MET cc_start: 0.1672 (mmp) cc_final: 0.1440 (tpp) REVERT: A 227 MET cc_start: 0.8998 (mpp) cc_final: 0.8083 (mpp) REVERT: A 309 THR cc_start: 0.7714 (m) cc_final: 0.7434 (t) REVERT: A 390 MET cc_start: 0.8892 (ttm) cc_final: 0.8682 (ttm) REVERT: A 511 MET cc_start: 0.7954 (tpt) cc_final: 0.7710 (tpp) REVERT: A 604 MET cc_start: 0.7880 (pmm) cc_final: 0.7557 (pmm) REVERT: A 683 MET cc_start: 0.7911 (ptt) cc_final: 0.7632 (ptt) REVERT: A 994 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7581 (tt0) REVERT: B 181 TYR cc_start: 0.8955 (t80) cc_final: 0.8636 (t80) REVERT: C 136 PHE cc_start: 0.7758 (p90) cc_final: 0.7200 (p90) REVERT: C 223 ILE cc_start: 0.9200 (tt) cc_final: 0.8922 (mp) REVERT: D 70 LEU cc_start: 0.8383 (mm) cc_final: 0.8134 (mm) REVERT: D 79 ARG cc_start: 0.9292 (mmt90) cc_final: 0.9001 (mmt90) REVERT: D 88 GLN cc_start: 0.9414 (tp40) cc_final: 0.9213 (tp40) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1255 time to fit residues: 27.9516 Evaluate side-chains 101 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 5 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 226 optimal weight: 0.0970 chunk 241 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN F 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056064 restraints weight = 110394.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057552 restraints weight = 64008.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058466 restraints weight = 45485.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059141 restraints weight = 36755.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.059526 restraints weight = 31822.015| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20780 Z= 0.134 Angle : 0.661 8.303 28106 Z= 0.346 Chirality : 0.045 0.250 3114 Planarity : 0.004 0.057 3646 Dihedral : 5.781 31.766 2730 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2502 helix: 0.64 (0.16), residues: 1157 sheet: -1.91 (0.31), residues: 262 loop : -2.74 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 132 TYR 0.018 0.001 TYR C 363 PHE 0.030 0.001 PHE B 277 TRP 0.082 0.002 TRP E 117 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00286 (20780) covalent geometry : angle 0.66117 (28106) hydrogen bonds : bond 0.03376 ( 825) hydrogen bonds : angle 4.53434 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 MET cc_start: 0.9215 (ptm) cc_final: 0.8863 (ppp) REVERT: E 203 TRP cc_start: 0.7753 (m-10) cc_final: 0.7374 (m100) REVERT: E 239 MET cc_start: 0.2502 (mmp) cc_final: 0.2252 (mmm) REVERT: A 227 MET cc_start: 0.8607 (mpp) cc_final: 0.8062 (mpp) REVERT: A 390 MET cc_start: 0.8906 (ttm) cc_final: 0.8701 (ttm) REVERT: A 511 MET cc_start: 0.7950 (tpt) cc_final: 0.7716 (tpp) REVERT: A 589 ASN cc_start: 0.7072 (p0) cc_final: 0.6116 (p0) REVERT: A 604 MET cc_start: 0.7833 (pmm) cc_final: 0.7563 (pmm) REVERT: A 683 MET cc_start: 0.7888 (ptt) cc_final: 0.7634 (ptt) REVERT: B 181 TYR cc_start: 0.8924 (t80) cc_final: 0.8405 (t80) REVERT: B 262 LEU cc_start: 0.9745 (mp) cc_final: 0.9487 (mm) REVERT: B 267 MET cc_start: 0.7650 (tmm) cc_final: 0.7418 (tmm) REVERT: B 436 ILE cc_start: 0.9055 (pt) cc_final: 0.8474 (mp) REVERT: C 136 PHE cc_start: 0.7709 (p90) cc_final: 0.7138 (p90) REVERT: C 265 MET cc_start: 0.9376 (mtm) cc_final: 0.8814 (mtt) REVERT: D 39 MET cc_start: 0.9056 (ttt) cc_final: 0.8786 (mmm) REVERT: D 70 LEU cc_start: 0.8253 (mm) cc_final: 0.7986 (mt) REVERT: D 79 ARG cc_start: 0.9228 (mmt90) cc_final: 0.8925 (mmt90) REVERT: D 88 GLN cc_start: 0.9418 (tp40) cc_final: 0.8754 (tp-100) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1200 time to fit residues: 27.7946 Evaluate side-chains 101 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 93 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 6 optimal weight: 6.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.078865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056797 restraints weight = 112854.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.058306 restraints weight = 65630.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059312 restraints weight = 46626.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.059950 restraints weight = 37495.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.060327 restraints weight = 32659.531| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20780 Z= 0.120 Angle : 0.658 8.746 28106 Z= 0.341 Chirality : 0.045 0.337 3114 Planarity : 0.004 0.057 3646 Dihedral : 5.561 32.281 2730 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.17), residues: 2502 helix: 0.74 (0.16), residues: 1145 sheet: -1.88 (0.31), residues: 252 loop : -2.65 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 132 TYR 0.029 0.001 TYR F 15 PHE 0.027 0.001 PHE C 362 TRP 0.079 0.002 TRP E 117 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00255 (20780) covalent geometry : angle 0.65789 (28106) hydrogen bonds : bond 0.03270 ( 825) hydrogen bonds : angle 4.44422 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 117 TRP cc_start: 0.7029 (m-90) cc_final: 0.6779 (m-90) REVERT: E 181 MET cc_start: 0.9200 (ptm) cc_final: 0.8836 (ppp) REVERT: E 239 MET cc_start: 0.2665 (mmp) cc_final: 0.2428 (mmm) REVERT: A 227 MET cc_start: 0.8560 (mpp) cc_final: 0.7794 (mpp) REVERT: A 390 MET cc_start: 0.8892 (ttm) cc_final: 0.8678 (ttp) REVERT: A 511 MET cc_start: 0.7939 (tpt) cc_final: 0.7681 (tpp) REVERT: A 589 ASN cc_start: 0.7047 (p0) cc_final: 0.6500 (p0) REVERT: A 604 MET cc_start: 0.7955 (pmm) cc_final: 0.7607 (pmm) REVERT: A 683 MET cc_start: 0.7853 (ptt) cc_final: 0.7587 (ptt) REVERT: B 181 TYR cc_start: 0.8869 (t80) cc_final: 0.8372 (t80) REVERT: B 267 MET cc_start: 0.7672 (tmm) cc_final: 0.7439 (tmm) REVERT: B 436 ILE cc_start: 0.9039 (pt) cc_final: 0.8474 (mp) REVERT: C 136 PHE cc_start: 0.7636 (p90) cc_final: 0.7063 (p90) REVERT: C 265 MET cc_start: 0.9360 (mtm) cc_final: 0.8779 (mtt) REVERT: C 275 ASP cc_start: 0.8065 (p0) cc_final: 0.7530 (p0) REVERT: D 39 MET cc_start: 0.9055 (ttt) cc_final: 0.8690 (mmm) REVERT: D 70 LEU cc_start: 0.8200 (mm) cc_final: 0.7925 (mt) REVERT: D 79 ARG cc_start: 0.9221 (mmt90) cc_final: 0.8905 (mmt90) REVERT: D 88 GLN cc_start: 0.9401 (tp40) cc_final: 0.8714 (tp-100) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1160 time to fit residues: 26.7154 Evaluate side-chains 100 residues out of total 2222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 246 optimal weight: 6.9990 chunk 201 optimal weight: 0.0270 chunk 209 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 140 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN B 102 ASN B 345 ASN B 379 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 102 ASN F 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.078370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056490 restraints weight = 111052.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057989 restraints weight = 64409.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058989 restraints weight = 45698.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059614 restraints weight = 36611.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059978 restraints weight = 31809.464| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20780 Z= 0.127 Angle : 0.650 9.159 28106 Z= 0.338 Chirality : 0.045 0.301 3114 Planarity : 0.004 0.057 3646 Dihedral : 5.516 32.179 2730 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.17), residues: 2502 helix: 0.80 (0.16), residues: 1144 sheet: -1.80 (0.32), residues: 252 loop : -2.62 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 132 TYR 0.034 0.001 TYR F 15 PHE 0.026 0.001 PHE C 92 TRP 0.078 0.002 TRP E 117 HIS 0.008 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00274 (20780) covalent geometry : angle 0.65028 (28106) hydrogen bonds : bond 0.03281 ( 825) hydrogen bonds : angle 4.41108 ( 2352) =============================================================================== Job complete usr+sys time: 3473.91 seconds wall clock time: 60 minutes 42.64 seconds (3642.64 seconds total)