Starting phenix.real_space_refine on Thu Jun 12 20:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yab_39094/06_2025/8yab_39094_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yab_39094/06_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_39094/06_2025/8yab_39094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yab_39094/06_2025/8yab_39094.map" model { file = "/net/cci-nas-00/data/ceres_data/8yab_39094/06_2025/8yab_39094_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yab_39094/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.83, per 1000 atoms: 0.69 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: 4.19 Conformation dependent library (CDL) restraints added in 2.4 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: 2.07 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: 5.30 Time building geometry restraints manager: 4.92 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- 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 : 1.689 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.2156 time to fit residues: 51.6227 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 : 1.811 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.077691 restraints weight = 82604.226| |-----------------------------------------------------------------------------| 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: 0.7006 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 : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 69 GLN cc_start: 0.7919 (mt0) cc_final: 0.7252 (mm110) REVERT: E 125 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8270 (mp) outliers start: 36 outliers final: 12 residues processed: 126 average time/residue: 0.1828 time to fit residues: 40.0879 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 : 1.631 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 127 optimal weight: 0.7980 chunk 77 optimal weight: 40.0000 chunk 224 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 0.0060 chunk 119 optimal weight: 0.8980 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.089967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077176 restraints weight = 82883.725| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 5.00 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1922 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= 0.142 Angle : 0.615 11.380 20013 Z= 0.300 Chirality : 0.042 0.237 2543 Planarity : 0.005 0.081 2663 Dihedral : 4.420 30.563 2321 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 3.21 % Allowed : 20.81 % Favored : 75.98 % 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: -0.36 (0.19), residues: 2204 helix: 1.08 (0.16), residues: 1070 sheet: -0.89 (0.38), residues: 189 loop : -1.68 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.005 0.001 HIS B 357 PHE 0.019 0.002 PHE E 51 TYR 0.016 0.002 TYR B 368 ARG 0.005 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 816) hydrogen bonds : angle 4.55334 ( 2373) covalent geometry : bond 0.00330 (14529) covalent geometry : angle 0.61534 (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 122 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 543 MET cc_start: 0.8657 (mmp) cc_final: 0.8323 (mmp) REVERT: C 69 GLN cc_start: 0.7922 (mt0) cc_final: 0.7167 (mm110) REVERT: E 125 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 31 outliers final: 12 residues processed: 117 average time/residue: 0.1735 time to fit residues: 36.3527 Evaluate side-chains 90 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 175 optimal weight: 0.2980 chunk 210 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.089185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.076336 restraints weight = 82782.239| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 5.00 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2209 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= 0.144 Angle : 0.605 11.323 20013 Z= 0.294 Chirality : 0.042 0.365 2543 Planarity : 0.005 0.081 2663 Dihedral : 4.240 30.170 2319 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 4.45 % Allowed : 21.53 % Favored : 74.02 % 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: -0.23 (0.19), residues: 2204 helix: 1.21 (0.16), residues: 1072 sheet: -0.94 (0.38), residues: 191 loop : -1.63 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 442 HIS 0.005 0.001 HIS B 357 PHE 0.022 0.002 PHE C 5 TYR 0.013 0.001 TYR A 654 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 816) hydrogen bonds : angle 4.44346 ( 2373) covalent geometry : bond 0.00337 (14529) covalent geometry : angle 0.60508 (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 124 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6507 (tmm-80) REVERT: B 543 MET cc_start: 0.8603 (mmp) cc_final: 0.8373 (mmp) REVERT: C 69 GLN cc_start: 0.7846 (mt0) cc_final: 0.7072 (mm110) REVERT: C 70 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8612 (mp10) REVERT: C 134 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7529 (tt) outliers start: 43 outliers final: 15 residues processed: 118 average time/residue: 0.1824 time to fit residues: 36.8213 Evaluate side-chains 95 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE 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 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 505 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 134 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: 5.9990 chunk 200 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 27 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 220 optimal weight: 30.0000 overall best weight: 2.7604 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.087334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.074388 restraints weight = 84399.209| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 5.03 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2475 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= 0.192 Angle : 0.640 10.621 20013 Z= 0.315 Chirality : 0.043 0.200 2543 Planarity : 0.005 0.081 2663 Dihedral : 4.438 31.177 2319 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 3.42 % Allowed : 22.88 % Favored : 73.71 % 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: -0.35 (0.19), residues: 2204 helix: 1.09 (0.16), residues: 1083 sheet: -1.04 (0.38), residues: 185 loop : -1.67 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 291 HIS 0.007 0.001 HIS B 357 PHE 0.018 0.002 PHE C 181 TYR 0.013 0.002 TYR E 326 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 816) hydrogen bonds : angle 4.56551 ( 2373) covalent geometry : bond 0.00439 (14529) covalent geometry : angle 0.64003 (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 107 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 728 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7271 (ptm160) REVERT: C 170 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9217 (mp) outliers start: 33 outliers final: 22 residues processed: 103 average time/residue: 0.1762 time to fit residues: 31.7233 Evaluate side-chains 95 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 728 ARG 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 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 170 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 128 VAL 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 339 VAL 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: 1.9990 chunk 102 optimal weight: 0.0470 chunk 190 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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** C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.088533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075697 restraints weight = 84632.355| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 5.06 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2660 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= 0.124 Angle : 0.591 10.601 20013 Z= 0.285 Chirality : 0.041 0.182 2543 Planarity : 0.005 0.081 2663 Dihedral : 4.136 30.433 2319 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer: Outliers : 3.83 % Allowed : 23.91 % Favored : 72.26 % 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: -0.09 (0.19), residues: 2204 helix: 1.29 (0.16), residues: 1092 sheet: -0.93 (0.39), residues: 185 loop : -1.55 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 291 HIS 0.004 0.001 HIS B 357 PHE 0.016 0.001 PHE C 5 TYR 0.012 0.001 TYR A 654 ARG 0.003 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 816) hydrogen bonds : angle 4.30213 ( 2373) covalent geometry : bond 0.00294 (14529) covalent geometry : angle 0.59123 (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 118 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 564 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6446 (t80) REVERT: C 69 GLN cc_start: 0.7864 (mt0) cc_final: 0.7233 (mm110) REVERT: C 150 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 170 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9209 (mp) outliers start: 37 outliers final: 21 residues processed: 112 average time/residue: 0.1823 time to fit residues: 36.0561 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 : 1.806 ------------------------------------------------------------------------------- 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 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR 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 E residue 29 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 271 CYS Chi-restraints excluded: chain E residue 339 VAL 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: 0.8980 chunk 128 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.088101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.075277 restraints weight = 84005.767| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.02 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2834 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= 0.134 Angle : 0.603 10.721 20013 Z= 0.288 Chirality : 0.041 0.197 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.079 30.619 2319 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 3.42 % Allowed : 24.64 % Favored : 71.95 % 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: -0.08 (0.19), residues: 2204 helix: 1.33 (0.16), residues: 1104 sheet: -0.88 (0.39), residues: 182 loop : -1.63 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 291 HIS 0.004 0.001 HIS B 357 PHE 0.015 0.001 PHE C 181 TYR 0.011 0.001 TYR A 654 ARG 0.002 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 816) hydrogen bonds : angle 4.25926 ( 2373) covalent geometry : bond 0.00314 (14529) covalent geometry : angle 0.60266 (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: 33 poor density : 74 time to evaluate : 1.782 Fit side-chains REVERT: A 471 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7920 (mp) REVERT: C 69 GLN cc_start: 0.7969 (mt0) cc_final: 0.7292 (mm110) REVERT: C 150 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 170 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9242 (mp) outliers start: 33 outliers final: 22 residues processed: 103 average time/residue: 0.1715 time to fit residues: 31.6685 Evaluate side-chains 93 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 451 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 481 THR 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 134 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain E residue 29 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 271 CYS 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: 6.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.086945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.074069 restraints weight = 84236.132| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 5.00 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3003 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= 0.160 Angle : 0.626 10.920 20013 Z= 0.302 Chirality : 0.042 0.208 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.221 31.363 2319 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.08 % Favored : 93.78 % Rotamer: Outliers : 3.93 % Allowed : 24.43 % Favored : 71.64 % 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: 1.28 (0.16), residues: 1106 sheet: -1.29 (0.37), residues: 192 loop : -1.62 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 231 HIS 0.005 0.001 HIS B 357 PHE 0.018 0.001 PHE C 29 TYR 0.025 0.002 TYR E 313 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 816) hydrogen bonds : angle 4.34572 ( 2373) covalent geometry : bond 0.00373 (14529) covalent geometry : angle 0.62588 (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 107 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 1.598 Fit side-chains REVERT: A 471 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 564 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6574 (t80) REVERT: C 69 GLN cc_start: 0.7876 (mt0) cc_final: 0.7253 (mm110) REVERT: C 150 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (tt) REVERT: C 170 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9277 (mp) outliers start: 38 outliers final: 27 residues processed: 102 average time/residue: 0.1770 time to fit residues: 31.7842 Evaluate side-chains 99 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 451 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 VAL 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 134 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain E residue 29 THR 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 216 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 271 CYS 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: 10.0000 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 131 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN C 68 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 = 0.4174 r_free = 0.4174 target = 0.089042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.076449 restraints weight = 83611.916| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 4.93 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 14529 Z= 0.104 Angle : 0.593 10.914 20013 Z= 0.279 Chirality : 0.041 0.173 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.832 30.221 2319 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 2.38 % Allowed : 25.67 % Favored : 71.95 % 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: 0.13 (0.19), residues: 2204 helix: 1.54 (0.16), residues: 1097 sheet: -1.06 (0.37), residues: 191 loop : -1.50 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 291 HIS 0.003 0.001 HIS E 269 PHE 0.016 0.001 PHE E 51 TYR 0.008 0.001 TYR A 654 ARG 0.002 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.02635 ( 816) hydrogen bonds : angle 4.07225 ( 2373) covalent geometry : bond 0.00245 (14529) covalent geometry : angle 0.59306 (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 103 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 564 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.5872 (t80) REVERT: C 69 GLN cc_start: 0.7840 (mt0) cc_final: 0.7348 (mm110) REVERT: C 150 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 0.1701 time to fit residues: 31.0236 Evaluate side-chains 90 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 422 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 70 GLN Chi-restraints excluded: chain C residue 150 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 216 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 271 CYS 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: 8.9990 chunk 113 optimal weight: 6.9990 chunk 125 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 218 optimal weight: 50.0000 chunk 85 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.087687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.074925 restraints weight = 83730.380| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 4.94 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3235 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= 0.143 Angle : 0.615 11.463 20013 Z= 0.292 Chirality : 0.041 0.184 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.908 30.618 2319 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.87 % Rotamer: Outliers : 2.17 % Allowed : 25.98 % Favored : 71.84 % 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: 1.58 (0.16), residues: 1099 sheet: -1.08 (0.38), residues: 191 loop : -1.49 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.004 0.001 HIS A 602 PHE 0.029 0.002 PHE C 5 TYR 0.020 0.001 TYR B 368 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 816) hydrogen bonds : angle 4.12513 ( 2373) covalent geometry : bond 0.00337 (14529) covalent geometry : angle 0.61471 (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 94 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 564 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6204 (t80) REVERT: C 69 GLN cc_start: 0.7815 (mt0) cc_final: 0.7230 (mm110) REVERT: C 70 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: C 150 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7962 (tt) outliers start: 21 outliers final: 16 residues processed: 91 average time/residue: 0.1638 time to fit residues: 27.1492 Evaluate side-chains 91 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 564 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 150 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 198 TRP Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 271 CYS 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: 0.4980 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** 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 = 0.4144 r_free = 0.4144 target = 0.087453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.074651 restraints weight = 84991.854| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.98 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3280 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= 0.142 Angle : 0.617 12.181 20013 Z= 0.293 Chirality : 0.042 0.186 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.947 30.807 2319 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.08 % Favored : 94.78 % Rotamer: Outliers : 2.28 % Allowed : 26.09 % Favored : 71.64 % 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: 0.15 (0.19), residues: 2204 helix: 1.56 (0.16), residues: 1100 sheet: -1.12 (0.38), residues: 191 loop : -1.49 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS A 602 PHE 0.028 0.002 PHE C 5 TYR 0.021 0.001 TYR B 368 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 816) hydrogen bonds : angle 4.14537 ( 2373) covalent geometry : bond 0.00336 (14529) covalent geometry : angle 0.61685 (20013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6211.91 seconds wall clock time: 107 minutes 16.25 seconds (6436.25 seconds total)