Starting phenix.real_space_refine on Fri May 16 09:22:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094.map" model { file = "/net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yab_39094/05_2025/8yab_39094_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 9022 2.51 5 N 2605 2.21 5 O 2638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14309 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 4219 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 286} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 632} Chain breaks: 9 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1097 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 16, 'PHE:plan': 13, 'GLU:plan': 34, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 647 Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3645 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 39, 'TRANS': 511} Chain breaks: 6 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 296 Chain: "C" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1295 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 169} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3114 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 434} Chain breaks: 5 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 711 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 288 Chain: "D" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2036 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 7 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1178 Unresolved non-hydrogen angles: 1525 Unresolved non-hydrogen dihedrals: 977 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 10, 'PHE:plan': 20, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 605 Time building chain proxies: 8.46, per 1000 atoms: 0.59 Number of scatterers: 14309 At special positions: 0 Unit cell: (108.8, 127.5, 166.6, 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 44 16.00 O 2638 8.00 N 2605 7.00 C 9022 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: 3.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 18 sheets defined 53.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.741A pdb=" N VAL A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.792A pdb=" N VAL A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.963A pdb=" N ALA A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 4.263A pdb=" N LYS A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.611A pdb=" N CYS A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.630A pdb=" N GLN A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.628A pdb=" N CYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.750A pdb=" N VAL A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 354 removed outlier: 4.384A pdb=" N TYR A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.533A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.588A pdb=" N ASN A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 443 removed outlier: 3.655A pdb=" N LYS A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 removed outlier: 5.127A pdb=" N VAL A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 463 through 473 removed outlier: 4.600A pdb=" N HIS A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.748A pdb=" N GLN A 516 " --> pdb=" O PRO A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.744A pdb=" N GLU A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.542A pdb=" N LEU A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.053A pdb=" N GLY A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 623 through 633 Processing helix chain 'A' and resid 633 through 640 removed outlier: 4.148A pdb=" N ILE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 664 through 683 removed outlier: 4.128A pdb=" N ILE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 710 removed outlier: 3.636A pdb=" N VAL A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 3.546A pdb=" N ARG A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.394A pdb=" N ALA A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 761 removed outlier: 4.443A pdb=" N LEU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.590A pdb=" N ALA A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 768 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.940A pdb=" N ALA B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.591A pdb=" N GLU B 30 " --> pdb=" O PRO B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 31 through 39 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.661A pdb=" N GLY B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 181 through 204 removed outlier: 3.538A pdb=" N LEU B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 278 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 304 through 307 removed outlier: 3.745A pdb=" N LEU B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.752A pdb=" N HIS B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.825A pdb=" N LEU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.670A pdb=" N LEU B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 454 removed outlier: 3.520A pdb=" N LEU B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 497 Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.630A pdb=" N PHE B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 530 Proline residue: B 518 - end of helix removed outlier: 4.041A pdb=" N ARG B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 548 removed outlier: 4.468A pdb=" N GLN B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET B 543 " --> pdb=" O TRP B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.950A pdb=" N THR B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 removed outlier: 4.073A pdb=" N LEU B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 removed outlier: 4.153A pdb=" N GLN B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 622 Processing helix chain 'B' and resid 623 through 630 removed outlier: 3.810A pdb=" N GLY B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 71 removed outlier: 4.180A pdb=" N ILE C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.630A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 removed outlier: 4.142A pdb=" N ILE C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'E' and resid 27 through 39 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 47 through 59 Processing helix chain 'E' and resid 125 through 143 removed outlier: 4.438A pdb=" N SER E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.129A pdb=" N GLN E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.767A pdb=" N LEU E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 276 through 282 Processing helix chain 'E' and resid 484 through 489 removed outlier: 4.420A pdb=" N LEU E 488 " --> pdb=" O THR E 484 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 489 " --> pdb=" O TYR E 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 484 through 489' Processing helix chain 'D' and resid 34 through 39 removed outlier: 3.572A pdb=" N MET D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.709A pdb=" N GLY D 123 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 144 Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.873A pdb=" N ASP D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 317 through 328 removed outlier: 4.145A pdb=" N TYR D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 352 removed outlier: 4.020A pdb=" N SER D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.647A pdb=" N ASP D 365 " --> pdb=" O TRP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 509 Processing helix chain 'D' and resid 510 through 520 removed outlier: 4.192A pdb=" N VAL D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 28 removed outlier: 3.781A pdb=" N ALA C 4 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 123 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 8 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 117 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 122 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 114 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 96 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.828A pdb=" N PHE C 106 " --> pdb=" O ALA C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 21 through 26 removed outlier: 6.308A pdb=" N LEU E 8 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER E 24 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 6 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARG E 26 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ARG E 4 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 5 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 107 " --> pdb=" O TRP E 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'E' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'E' and resid 216 through 220 Processing sheet with id=AA7, first strand: chain 'E' and resid 253 through 254 removed outlier: 3.563A pdb=" N SER E 253 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 322 through 325 removed outlier: 3.624A pdb=" N ASN E 340 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 328 through 330 removed outlier: 4.058A pdb=" N LYS E 329 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 336 " --> pdb=" O LYS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 356 through 357 removed outlier: 3.737A pdb=" N ILE E 430 " --> pdb=" O ILE E 474 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 474 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 369 through 370 removed outlier: 3.946A pdb=" N GLU E 370 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 77 through 80 removed outlier: 3.531A pdb=" N GLY D 55 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA D 45 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER D 475 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 47 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 88 removed outlier: 4.188A pdb=" N HIS D 86 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 105 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU D 117 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE D 129 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 119 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA D 127 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 154 through 160 removed outlier: 6.433A pdb=" N ILE D 156 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE D 167 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 158 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 165 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 173 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE D 191 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN D 189 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 207 removed outlier: 6.409A pdb=" N LEU D 216 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR D 206 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE D 214 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 215 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.674A pdb=" N ALA D 271 " --> pdb=" O LEU D 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 280 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 428 through 432 removed outlier: 5.242A pdb=" N CYS D 429 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR D 440 " --> pdb=" O CYS D 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 481 through 484 removed outlier: 3.845A pdb=" N CYS D 481 " --> pdb=" O ILE D 492 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2373 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: 4.67 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 10 1.17 - 1.33: 3281 1.33 - 1.49: 5205 1.49 - 1.65: 5980 1.65 - 1.81: 53 Bond restraints: 14529 Sorted by residual: bond pdb=" CG PRO E 482 " pdb=" CD PRO E 482 " ideal model delta sigma weight residual 1.503 1.084 0.419 3.40e-02 8.65e+02 1.52e+02 bond pdb=" CA ARG C 22 " pdb=" C ARG C 22 " ideal model delta sigma weight residual 1.523 1.390 0.133 1.23e-02 6.61e+03 1.16e+02 bond pdb=" CG PRO B 437 " pdb=" CD PRO B 437 " ideal model delta sigma weight residual 1.503 1.150 0.353 3.40e-02 8.65e+02 1.08e+02 bond pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 1.492 1.009 0.483 5.00e-02 4.00e+02 9.34e+01 bond pdb=" C TYR D 323 " pdb=" O TYR D 323 " ideal model delta sigma weight residual 1.236 1.112 0.124 1.29e-02 6.01e+03 9.29e+01 ... (remaining 14524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.37: 19998 13.37 - 26.74: 9 26.74 - 40.11: 5 40.11 - 53.48: 0 53.48 - 66.85: 1 Bond angle restraints: 20013 Sorted by residual: angle pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " pdb=" CD PRO B 376 " ideal model delta sigma weight residual 106.10 172.95 -66.85 3.20e+00 9.77e-02 4.36e+02 angle pdb=" N PRO B 437 " pdb=" CD PRO B 437 " pdb=" CG PRO B 437 " ideal model delta sigma weight residual 103.20 72.40 30.80 1.50e+00 4.44e-01 4.22e+02 angle pdb=" CA PRO B 437 " pdb=" CB PRO B 437 " pdb=" CG PRO B 437 " ideal model delta sigma weight residual 104.50 67.11 37.39 1.90e+00 2.77e-01 3.87e+02 angle pdb=" N PRO B 376 " pdb=" CD PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 103.20 76.05 27.15 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CA PRO B 376 " pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 104.50 73.73 30.77 1.90e+00 2.77e-01 2.62e+02 ... (remaining 20008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 7814 16.00 - 32.00: 620 32.00 - 48.00: 163 48.00 - 63.99: 33 63.99 - 79.99: 12 Dihedral angle restraints: 8642 sinusoidal: 2073 harmonic: 6569 Sorted by residual: dihedral pdb=" C ARG D 336 " pdb=" N ARG D 336 " pdb=" CA ARG D 336 " pdb=" CB ARG D 336 " ideal model delta harmonic sigma weight residual -122.60 -140.82 18.22 0 2.50e+00 1.60e-01 5.31e+01 dihedral pdb=" C PHE D 332 " pdb=" N PHE D 332 " pdb=" CA PHE D 332 " pdb=" CB PHE D 332 " ideal model delta harmonic sigma weight residual -122.60 -140.12 17.52 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" N PHE D 332 " pdb=" C PHE D 332 " pdb=" CA PHE D 332 " pdb=" CB PHE D 332 " ideal model delta harmonic sigma weight residual 122.80 139.50 -16.70 0 2.50e+00 1.60e-01 4.46e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 2532 0.196 - 0.392: 4 0.392 - 0.588: 4 0.588 - 0.785: 2 0.785 - 0.981: 1 Chirality restraints: 2543 Sorted by residual: chirality pdb=" CA ARG D 336 " pdb=" N ARG D 336 " pdb=" C ARG D 336 " pdb=" CB ARG D 336 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA PHE D 332 " pdb=" N PHE D 332 " pdb=" C PHE D 332 " pdb=" CB PHE D 332 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA SER D 331 " pdb=" N SER D 331 " pdb=" C SER D 331 " pdb=" CB SER D 331 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 2540 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 22 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ARG C 22 " 0.094 2.00e-02 2.50e+03 pdb=" O ARG C 22 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL C 23 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 481 " -0.072 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 482 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 482 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 482 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 336 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ARG D 336 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG D 336 " -0.022 2.00e-02 2.50e+03 pdb=" N SER D 337 " -0.019 2.00e-02 2.50e+03 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 12 2.20 - 2.87: 5489 2.87 - 3.55: 20468 3.55 - 4.22: 28796 4.22 - 4.90: 49650 Nonbonded interactions: 104415 Sorted by model distance: nonbonded pdb=" CD2 LEU C 48 " pdb=" CB TYR D 323 " model vdw 1.521 3.860 nonbonded pdb=" O GLU C 103 " pdb=" O PHE D 332 " model vdw 1.779 3.040 nonbonded pdb=" CB LEU C 49 " pdb=" CD1 LEU D 327 " model vdw 1.801 3.860 nonbonded pdb=" NH2 ARG C 59 " pdb=" N ASP D 316 " model vdw 2.120 3.200 nonbonded pdb=" CG LEU C 49 " pdb=" CD1 LEU D 327 " model vdw 2.121 3.890 ... (remaining 104410 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 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 : 0.010 0.483 14529 Z= 0.403 Angle : 1.158 66.846 20013 Z= 0.592 Chirality : 0.058 0.981 2543 Planarity : 0.007 0.101 2663 Dihedral : 13.953 79.993 4336 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.94 % Favored : 91.61 % Rotamer: Outliers : 0.93 % Allowed : 19.88 % Favored : 79.19 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2204 helix: 0.56 (0.16), residues: 1045 sheet: -1.23 (0.39), residues: 178 loop : -1.89 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 114 HIS 0.008 0.002 HIS B 357 PHE 0.018 0.002 PHE E 37 TYR 0.025 0.002 TYR B 368 ARG 0.013 0.001 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.15949 ( 816) hydrogen bonds : angle 6.42562 ( 2373) covalent geometry : bond 0.00961 (14529) covalent geometry : angle 1.15805 (20013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.758 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.2117 time to fit residues: 50.7338 Evaluate side-chains 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 318 PRO Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 337 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.090521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.077695 restraints weight = 82604.239| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.01 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 14529 Z= 0.174 Angle : 0.707 16.781 20013 Z= 0.345 Chirality : 0.043 0.203 2543 Planarity : 0.006 0.081 2663 Dihedral : 4.874 37.646 2328 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.90 % Favored : 93.92 % Rotamer: Outliers : 3.73 % Allowed : 20.60 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2204 helix: 0.78 (0.16), residues: 1073 sheet: -1.10 (0.37), residues: 203 loop : -1.74 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 225 HIS 0.005 0.001 HIS B 357 PHE 0.020 0.002 PHE E 51 TYR 0.015 0.002 TYR A 654 ARG 0.008 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 816) hydrogen bonds : angle 4.94998 ( 2373) covalent geometry : bond 0.00410 (14529) covalent geometry : angle 0.70680 (20013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 69 GLN cc_start: 0.7925 (mt0) cc_final: 0.7257 (mm110) REVERT: E 125 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8270 (mp) outliers start: 36 outliers final: 12 residues processed: 126 average time/residue: 0.1687 time to fit residues: 37.0551 Evaluate side-chains 95 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 127 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 119 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN C 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.091741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.079057 restraints weight = 82166.940| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 5.03 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14529 Z= 0.115 Angle : 0.603 11.847 20013 Z= 0.290 Chirality : 0.041 0.223 2543 Planarity : 0.005 0.079 2663 Dihedral : 4.273 30.189 2321 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer: Outliers : 2.69 % Allowed : 21.33 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 2204 helix: 1.20 (0.16), residues: 1059 sheet: -0.84 (0.38), residues: 188 loop : -1.63 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.005 0.001 HIS B 365 PHE 0.019 0.001 PHE E 51 TYR 0.013 0.001 TYR A 654 ARG 0.004 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 816) hydrogen bonds : angle 4.47203 ( 2373) covalent geometry : bond 0.00264 (14529) covalent geometry : angle 0.60254 (20013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 543 MET cc_start: 0.8592 (mmp) cc_final: 0.8257 (mmp) REVERT: C 69 GLN cc_start: 0.7793 (mt0) cc_final: 0.7074 (mm110) REVERT: E 125 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 26 outliers final: 6 residues processed: 120 average time/residue: 0.1679 time to fit residues: 35.4638 Evaluate side-chains 88 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 210 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 182 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 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 = 0.4206 r_free = 0.4206 target = 0.091405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.078683 restraints weight = 82059.469| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 5.04 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14529 Z= 0.113 Angle : 0.587 11.075 20013 Z= 0.280 Chirality : 0.042 0.424 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.996 29.034 2319 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 3.42 % Allowed : 21.01 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 2204 helix: 1.41 (0.16), residues: 1074 sheet: -0.74 (0.38), residues: 190 loop : -1.57 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS A 602 PHE 0.025 0.001 PHE C 5 TYR 0.018 0.001 TYR B 615 ARG 0.003 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 816) hydrogen bonds : angle 4.26438 ( 2373) covalent geometry : bond 0.00266 (14529) covalent geometry : angle 0.58678 (20013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 483 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 728 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6412 (tmm-80) REVERT: C 69 GLN cc_start: 0.7778 (mt0) cc_final: 0.7097 (mm110) REVERT: E 125 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (mp) REVERT: D 335 ASP cc_start: 0.8310 (t0) cc_final: 0.8065 (t0) outliers start: 33 outliers final: 13 residues processed: 116 average time/residue: 0.1800 time to fit residues: 36.8216 Evaluate side-chains 95 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 91 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.088006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.075088 restraints weight = 84007.073| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 5.01 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14529 Z= 0.187 Angle : 0.653 10.923 20013 Z= 0.319 Chirality : 0.043 0.344 2543 Planarity : 0.005 0.079 2663 Dihedral : 4.353 30.590 2319 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 3.52 % Allowed : 22.26 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2204 helix: 1.23 (0.16), residues: 1088 sheet: -0.97 (0.37), residues: 191 loop : -1.64 (0.22), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 442 HIS 0.009 0.001 HIS B 357 PHE 0.016 0.002 PHE C 29 TYR 0.017 0.002 TYR E 27 ARG 0.003 0.000 ARG E 363 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 816) hydrogen bonds : angle 4.50193 ( 2373) covalent geometry : bond 0.00430 (14529) covalent geometry : angle 0.65325 (20013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7210 (ptm160) REVERT: C 69 GLN cc_start: 0.7912 (mt0) cc_final: 0.7231 (mm110) REVERT: C 150 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7960 (tt) REVERT: C 170 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9133 (mp) REVERT: C 180 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.4165 (mt) REVERT: D 335 ASP cc_start: 0.8566 (t0) cc_final: 0.8346 (t0) outliers start: 34 outliers final: 21 residues processed: 110 average time/residue: 0.1879 time to fit residues: 35.8601 Evaluate side-chains 99 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 5 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 190 optimal weight: 0.0010 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.089593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.076827 restraints weight = 84213.608| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 5.01 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14529 Z= 0.113 Angle : 0.589 10.516 20013 Z= 0.280 Chirality : 0.041 0.337 2543 Planarity : 0.005 0.078 2663 Dihedral : 4.000 29.175 2319 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.17 % Favored : 95.69 % Rotamer: Outliers : 3.00 % Allowed : 22.77 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2204 helix: 1.48 (0.16), residues: 1084 sheet: -0.87 (0.38), residues: 191 loop : -1.52 (0.22), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 442 HIS 0.003 0.001 HIS A 412 PHE 0.018 0.001 PHE C 5 TYR 0.012 0.001 TYR A 654 ARG 0.006 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 816) hydrogen bonds : angle 4.20788 ( 2373) covalent geometry : bond 0.00265 (14529) covalent geometry : angle 0.58929 (20013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6502 (tmm-80) REVERT: C 69 GLN cc_start: 0.7797 (mt0) cc_final: 0.7242 (mm110) REVERT: C 150 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7992 (tt) REVERT: C 180 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4078 (mt) REVERT: D 335 ASP cc_start: 0.8490 (t0) cc_final: 0.8203 (t0) outliers start: 29 outliers final: 12 residues processed: 109 average time/residue: 0.1794 time to fit residues: 34.2479 Evaluate side-chains 92 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 124 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 123 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.088845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.076110 restraints weight = 83515.867| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 4.94 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14529 Z= 0.130 Angle : 0.606 11.003 20013 Z= 0.285 Chirality : 0.042 0.337 2543 Planarity : 0.005 0.078 2663 Dihedral : 3.972 29.838 2319 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 2.69 % Allowed : 23.71 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 2204 helix: 1.49 (0.16), residues: 1087 sheet: -0.89 (0.38), residues: 191 loop : -1.52 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.004 0.001 HIS B 357 PHE 0.019 0.001 PHE A 565 TYR 0.011 0.001 TYR E 27 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 816) hydrogen bonds : angle 4.20274 ( 2373) covalent geometry : bond 0.00307 (14529) covalent geometry : angle 0.60552 (20013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 728 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6479 (tmm-80) REVERT: C 69 GLN cc_start: 0.7823 (mt0) cc_final: 0.7192 (mm110) REVERT: C 70 GLN cc_start: 0.8603 (mt0) cc_final: 0.8380 (mp10) REVERT: C 150 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 180 LEU cc_start: 0.4423 (OUTLIER) cc_final: 0.4098 (mt) REVERT: D 335 ASP cc_start: 0.8516 (t0) cc_final: 0.8219 (t0) outliers start: 26 outliers final: 20 residues processed: 103 average time/residue: 0.1740 time to fit residues: 31.5645 Evaluate side-chains 101 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 57 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.086626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.073725 restraints weight = 84283.124| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.97 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14529 Z= 0.182 Angle : 0.655 10.832 20013 Z= 0.316 Chirality : 0.043 0.335 2543 Planarity : 0.005 0.078 2663 Dihedral : 4.363 31.382 2319 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % Rotamer: Outliers : 3.00 % Allowed : 24.33 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 2204 helix: 1.31 (0.16), residues: 1086 sheet: -1.15 (0.38), residues: 190 loop : -1.53 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 231 HIS 0.008 0.001 HIS B 357 PHE 0.025 0.002 PHE A 565 TYR 0.014 0.002 TYR E 326 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 816) hydrogen bonds : angle 4.46380 ( 2373) covalent geometry : bond 0.00420 (14529) covalent geometry : angle 0.65468 (20013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.594 Fit side-chains REVERT: C 69 GLN cc_start: 0.7939 (mt0) cc_final: 0.7140 (mm110) REVERT: C 150 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7988 (tt) REVERT: C 180 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4348 (mt) REVERT: D 335 ASP cc_start: 0.8568 (t0) cc_final: 0.8314 (t0) outliers start: 29 outliers final: 24 residues processed: 94 average time/residue: 0.1776 time to fit residues: 29.2704 Evaluate side-chains 94 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 207 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.088607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.075938 restraints weight = 83517.877| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.93 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14529 Z= 0.110 Angle : 0.599 10.722 20013 Z= 0.280 Chirality : 0.041 0.350 2543 Planarity : 0.004 0.076 2663 Dihedral : 3.925 30.514 2319 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 2.38 % Allowed : 25.16 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2204 helix: 1.59 (0.16), residues: 1085 sheet: -1.12 (0.37), residues: 197 loop : -1.43 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 291 HIS 0.003 0.001 HIS E 357 PHE 0.022 0.001 PHE A 565 TYR 0.009 0.001 TYR A 654 ARG 0.003 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 816) hydrogen bonds : angle 4.13586 ( 2373) covalent geometry : bond 0.00263 (14529) covalent geometry : angle 0.59878 (20013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: C 69 GLN cc_start: 0.7953 (mt0) cc_final: 0.7355 (mm110) REVERT: C 150 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7993 (tt) REVERT: C 180 LEU cc_start: 0.4737 (OUTLIER) cc_final: 0.4168 (mt) REVERT: D 335 ASP cc_start: 0.8475 (t0) cc_final: 0.8188 (t0) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.1847 time to fit residues: 30.4816 Evaluate side-chains 89 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 207 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 218 optimal weight: 50.0000 chunk 85 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.087591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.074824 restraints weight = 83661.494| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 4.92 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14529 Z= 0.139 Angle : 0.614 10.563 20013 Z= 0.292 Chirality : 0.042 0.341 2543 Planarity : 0.005 0.076 2663 Dihedral : 3.959 30.670 2319 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 2.07 % Allowed : 25.26 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2204 helix: 1.57 (0.16), residues: 1092 sheet: -1.12 (0.37), residues: 197 loop : -1.46 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 231 HIS 0.003 0.001 HIS A 602 PHE 0.025 0.001 PHE A 565 TYR 0.009 0.001 TYR E 326 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 816) hydrogen bonds : angle 4.18743 ( 2373) covalent geometry : bond 0.00326 (14529) covalent geometry : angle 0.61442 (20013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 564 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6198 (t80) REVERT: C 69 GLN cc_start: 0.7933 (mt0) cc_final: 0.7313 (mm110) REVERT: C 150 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 180 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4356 (mt) REVERT: D 335 ASP cc_start: 0.8510 (t0) cc_final: 0.8191 (t0) outliers start: 20 outliers final: 16 residues processed: 85 average time/residue: 0.1754 time to fit residues: 27.0208 Evaluate side-chains 86 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 218 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 128 optimal weight: 0.0060 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.087690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.074930 restraints weight = 84781.449| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.97 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14529 Z= 0.128 Angle : 0.610 15.365 20013 Z= 0.287 Chirality : 0.041 0.177 2543 Planarity : 0.004 0.076 2663 Dihedral : 3.906 30.739 2319 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.54 % Favored : 95.33 % Rotamer: Outliers : 2.07 % Allowed : 25.47 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2204 helix: 1.61 (0.16), residues: 1092 sheet: -1.07 (0.38), residues: 197 loop : -1.45 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS B 357 PHE 0.028 0.001 PHE A 565 TYR 0.009 0.001 TYR A 654 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 816) hydrogen bonds : angle 4.15829 ( 2373) covalent geometry : bond 0.00303 (14529) covalent geometry : angle 0.60988 (20013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.17 seconds wall clock time: 98 minutes 28.07 seconds (5908.07 seconds total)