Starting phenix.real_space_refine on Fri May 16 09:26:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.map" model { file = "/net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yah_39099/05_2025/8yah_39099.cif" } resolution = 3.3 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 9022 2.51 5 N 2605 2.21 5 O 2638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14309 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 4219 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 286} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 632} Chain breaks: 9 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1097 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 16, 'PHE:plan': 13, 'GLU:plan': 34, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 647 Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3645 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 39, 'TRANS': 511} Chain breaks: 6 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 296 Chain: "C" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1295 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 169} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3114 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 434} Chain breaks: 5 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 711 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 288 Chain: "D" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2036 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 7 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1178 Unresolved non-hydrogen angles: 1525 Unresolved non-hydrogen dihedrals: 977 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 10, 'PHE:plan': 20, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 605 Time building chain proxies: 10.88, per 1000 atoms: 0.76 Number of scatterers: 14309 At special positions: 0 Unit cell: (117.3, 126.65, 164.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2638 8.00 N 2605 7.00 C 9022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 2.3 seconds 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 18 sheets defined 53.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 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: 3.742A pdb=" N VAL A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.791A 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: 4.262A 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: 3.656A 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: 4.599A 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: 3.743A pdb=" N GLU A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.541A 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: 3.716A 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: 3.635A pdb=" N VAL A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.124A 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: 4.557A pdb=" N SER A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.986A 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: 4.444A 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: 4.139A 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: 4.023A 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: 3.592A 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: 3.744A 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: 3.751A 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: 4.495A 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: 3.660A pdb=" N LEU B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 4.172A 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: 3.629A 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: 4.117A 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: 4.179A pdb=" N ILE C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.631A 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: 3.573A pdb=" N MET D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.708A 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: 4.144A pdb=" N TYR D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 4.015A 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: 3.780A pdb=" N ALA C 4 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.576A 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: 3.621A 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: 3.848A 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: 6.309A 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: 3.697A 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: 3.625A 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: 4.057A 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: 7.141A 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: 6.935A 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: 6.434A pdb=" N ILE D 156 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE D 167 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.611A pdb=" N ILE D 173 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 4.081A 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: 6.597A 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: 5.22 Time building geometry restraints manager: 4.40 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: 3279 1.33 - 1.49: 5206 1.49 - 1.65: 5981 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 1.17e+02 bond pdb=" CG PRO B 437 " pdb=" CD PRO B 437 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+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 9.35e+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 9.25e+01 ... (remaining 14524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.38: 19998 13.38 - 26.75: 9 26.75 - 40.13: 5 40.13 - 53.50: 0 53.50 - 66.88: 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 106.10 172.98 -66.88 3.20e+00 9.77e-02 4.37e+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 72.38 30.82 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 67.10 37.40 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 73.70 30.80 1.90e+00 2.77e-01 2.63e+02 ... (remaining 20008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 7815 16.00 - 32.01: 619 32.01 - 48.01: 163 48.01 - 64.02: 33 64.02 - 80.02: 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 -140.86 18.26 0 2.50e+00 1.60e-01 5.34e+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 -140.13 17.53 0 2.50e+00 1.60e-01 4.92e+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 122.80 139.52 -16.72 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 2532 0.197 - 0.393: 4 0.393 - 0.590: 4 0.590 - 0.786: 2 0.786 - 0.983: 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 2.41e+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 1.08e+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 5.43e-02 2.95e+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 1.65e+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: 5492 2.87 - 3.55: 20472 3.55 - 4.22: 28787 4.22 - 4.90: 49657 Nonbonded interactions: 104420 Sorted by model distance: nonbonded pdb=" CD2 LEU C 48 " pdb=" CB TYR D 323 " model vdw 1.522 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 104415 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: 13.230 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 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= 0.404 Angle : 1.159 66.876 20013 Z= 0.593 Chirality : 0.058 0.983 2543 Planarity : 0.007 0.101 2663 Dihedral : 13.954 80.023 4336 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.85 % Favored : 91.70 % Rotamer: Outliers : 0.72 % Allowed : 20.08 % 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: 0.55 (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 0.024 0.002 TRP C 114 HIS 0.008 0.002 HIS B 357 PHE 0.018 0.002 PHE E 37 TYR 0.025 0.003 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 6.42626 ( 2373) covalent geometry : bond 0.00962 (14529) covalent geometry : angle 1.15856 (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 150 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 SER cc_start: -0.3514 (OUTLIER) cc_final: -0.4280 (p) REVERT: C 5 PHE cc_start: 0.4190 (t80) cc_final: 0.3879 (t80) outliers start: 7 outliers final: 3 residues processed: 150 average time/residue: 0.2352 time to fit residues: 53.7613 Evaluate side-chains 88 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER 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: 9.9990 chunk 171 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 40.0000 chunk 177 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.0270 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 0.0020 overall best weight: 0.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** 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 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.096702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.086142 restraints weight = 107619.538| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 6.59 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14529 Z= 0.135 Angle : 0.695 17.077 20013 Z= 0.333 Chirality : 0.043 0.191 2543 Planarity : 0.006 0.080 2663 Dihedral : 4.543 39.993 2326 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.54 % Favored : 95.28 % Rotamer: Outliers : 2.59 % Allowed : 19.05 % Favored : 78.36 % 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: -0.47 (0.19), residues: 2204 helix: 0.96 (0.16), residues: 1068 sheet: -1.17 (0.38), residues: 184 loop : -1.63 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 225 HIS 0.005 0.001 HIS B 611 PHE 0.021 0.002 PHE E 51 TYR 0.021 0.001 TYR A 654 ARG 0.008 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 816) hydrogen bonds : angle 4.82040 ( 2373) covalent geometry : bond 0.00303 (14529) covalent geometry : angle 0.69450 (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 128 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8959 (mm) cc_final: 0.8656 (mm) REVERT: A 484 GLN cc_start: 0.5440 (tm-30) cc_final: 0.5227 (tm-30) REVERT: B 343 ASP cc_start: 0.8866 (t0) cc_final: 0.8640 (t0) REVERT: B 515 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8286 (tp) outliers start: 25 outliers final: 4 residues processed: 124 average time/residue: 0.2067 time to fit residues: 41.2150 Evaluate side-chains 90 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN B 183 GLN ** 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 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.086983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.075782 restraints weight = 109820.626| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 6.36 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14529 Z= 0.291 Angle : 0.820 12.369 20013 Z= 0.419 Chirality : 0.049 0.299 2543 Planarity : 0.006 0.084 2663 Dihedral : 5.298 32.015 2319 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.30 % Favored : 92.56 % Rotamer: Outliers : 4.55 % Allowed : 18.94 % Favored : 76.50 % 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: -1.13 (0.18), residues: 2204 helix: 0.40 (0.16), residues: 1084 sheet: -1.78 (0.35), residues: 199 loop : -1.91 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.005 TRP B 65 HIS 0.009 0.002 HIS A 402 PHE 0.040 0.003 PHE C 29 TYR 0.029 0.003 TYR E 27 ARG 0.033 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.05407 ( 816) hydrogen bonds : angle 5.31995 ( 2373) covalent geometry : bond 0.00593 (14529) covalent geometry : angle 0.81987 (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 131 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 GLN cc_start: 0.6132 (tm-30) cc_final: 0.5862 (tm-30) REVERT: E 80 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6804 (ptmm) outliers start: 44 outliers final: 18 residues processed: 125 average time/residue: 0.1864 time to fit residues: 38.8356 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 : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 80 LYS 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 390 ILE Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 163 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 210 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.089071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.077971 restraints weight = 107568.159| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 6.28 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.4375 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= 0.123 Angle : 0.605 12.060 20013 Z= 0.293 Chirality : 0.042 0.354 2543 Planarity : 0.005 0.082 2663 Dihedral : 4.139 28.921 2319 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 20.39 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2204 helix: 1.16 (0.16), residues: 1081 sheet: -1.51 (0.36), residues: 185 loop : -1.61 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 65 HIS 0.003 0.001 HIS B 540 PHE 0.021 0.002 PHE E 51 TYR 0.015 0.001 TYR A 654 ARG 0.007 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 816) hydrogen bonds : angle 4.40571 ( 2373) covalent geometry : bond 0.00259 (14529) covalent geometry : angle 0.60467 (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 104 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9012 (mm) cc_final: 0.8711 (mm) REVERT: B 343 ASP cc_start: 0.8682 (t0) cc_final: 0.8481 (t0) REVERT: E 198 TRP cc_start: 0.7742 (p90) cc_final: 0.7483 (p90) outliers start: 22 outliers final: 6 residues processed: 98 average time/residue: 0.1838 time to fit residues: 30.8253 Evaluate side-chains 81 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 252 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 91 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 212 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.083022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.071848 restraints weight = 111286.821| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 6.18 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 14529 Z= 0.271 Angle : 0.801 10.033 20013 Z= 0.402 Chirality : 0.047 0.254 2543 Planarity : 0.006 0.086 2663 Dihedral : 5.200 31.185 2319 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 3.73 % Allowed : 19.25 % Favored : 77.02 % 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: -1.03 (0.18), residues: 2204 helix: 0.53 (0.16), residues: 1102 sheet: -1.61 (0.37), residues: 176 loop : -2.01 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 295 HIS 0.006 0.002 HIS B 621 PHE 0.029 0.003 PHE B 466 TYR 0.016 0.003 TYR B 615 ARG 0.006 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 816) hydrogen bonds : angle 5.21114 ( 2373) covalent geometry : bond 0.00593 (14529) covalent geometry : angle 0.80140 (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 109 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 1.483 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 104 average time/residue: 0.1756 time to fit residues: 31.5914 Evaluate side-chains 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 88 VAL 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 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4461 r_free = 0.4461 target = 0.084509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.073301 restraints weight = 110685.348| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 6.27 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14529 Z= 0.139 Angle : 0.623 9.021 20013 Z= 0.303 Chirality : 0.043 0.364 2543 Planarity : 0.005 0.084 2663 Dihedral : 4.411 31.262 2319 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 2.38 % Allowed : 21.74 % Favored : 75.88 % 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: -0.57 (0.19), residues: 2204 helix: 0.98 (0.16), residues: 1100 sheet: -1.82 (0.36), residues: 188 loop : -1.76 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 7 HIS 0.003 0.001 HIS B 357 PHE 0.018 0.002 PHE E 51 TYR 0.017 0.001 TYR B 60 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 816) hydrogen bonds : angle 4.54890 ( 2373) covalent geometry : bond 0.00309 (14529) covalent geometry : angle 0.62267 (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 97 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9020 (mm) cc_final: 0.8748 (mm) REVERT: A 544 MET cc_start: 0.5710 (pmm) cc_final: 0.5180 (ptm) REVERT: E 179 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6588 (m-40) outliers start: 23 outliers final: 13 residues processed: 93 average time/residue: 0.1821 time to fit residues: 29.9774 Evaluate side-chains 82 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 124 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 123 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 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 = 0.4478 r_free = 0.4478 target = 0.085113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.074019 restraints weight = 109264.228| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 6.27 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.6366 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= 0.117 Angle : 0.588 9.250 20013 Z= 0.280 Chirality : 0.041 0.259 2543 Planarity : 0.005 0.085 2663 Dihedral : 3.922 31.057 2319 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 2.38 % Allowed : 21.74 % Favored : 75.88 % 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: 1.36 (0.16), residues: 1098 sheet: -1.50 (0.39), residues: 176 loop : -1.66 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 7 HIS 0.003 0.001 HIS C 149 PHE 0.013 0.001 PHE B 466 TYR 0.016 0.001 TYR B 60 ARG 0.008 0.001 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 816) hydrogen bonds : angle 4.22236 ( 2373) covalent geometry : bond 0.00271 (14529) covalent geometry : angle 0.58825 (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 99 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8972 (mm) cc_final: 0.8737 (mm) REVERT: A 544 MET cc_start: 0.5608 (pmm) cc_final: 0.5029 (ptm) REVERT: C 11 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.3960 (mmm160) REVERT: E 179 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6591 (m-40) REVERT: D 331 SER cc_start: 0.6661 (OUTLIER) cc_final: 0.6454 (t) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.1837 time to fit residues: 30.3390 Evaluate side-chains 84 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 57 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 158 optimal weight: 0.0040 chunk 53 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 69 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 = 0.4474 r_free = 0.4474 target = 0.084966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.073897 restraints weight = 109679.384| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 6.26 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14529 Z= 0.114 Angle : 0.586 8.556 20013 Z= 0.278 Chirality : 0.041 0.246 2543 Planarity : 0.005 0.085 2663 Dihedral : 3.764 30.274 2319 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 1.76 % Allowed : 22.77 % Favored : 75.47 % 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: 0.05 (0.19), residues: 2204 helix: 1.51 (0.16), residues: 1102 sheet: -1.44 (0.39), residues: 181 loop : -1.52 (0.22), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 295 HIS 0.003 0.001 HIS B 611 PHE 0.014 0.001 PHE A 408 TYR 0.014 0.001 TYR B 60 ARG 0.006 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 816) hydrogen bonds : angle 4.12570 ( 2373) covalent geometry : bond 0.00267 (14529) covalent geometry : angle 0.58588 (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 89 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9021 (mm) cc_final: 0.8806 (mm) REVERT: C 64 MET cc_start: 0.4227 (ttm) cc_final: 0.4012 (ttm) outliers start: 17 outliers final: 10 residues processed: 83 average time/residue: 0.1715 time to fit residues: 25.6587 Evaluate side-chains 79 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 236 THR 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: 7.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 211 optimal weight: 0.0000 chunk 17 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** C 69 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 = 0.4479 r_free = 0.4479 target = 0.085104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.074169 restraints weight = 109097.913| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 6.13 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14529 Z= 0.108 Angle : 0.573 8.757 20013 Z= 0.270 Chirality : 0.041 0.213 2543 Planarity : 0.004 0.085 2663 Dihedral : 3.630 29.435 2319 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.78 % Rotamer: Outliers : 1.55 % Allowed : 22.67 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2204 helix: 1.65 (0.16), residues: 1106 sheet: -1.24 (0.40), residues: 183 loop : -1.42 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 198 HIS 0.003 0.001 HIS C 149 PHE 0.012 0.001 PHE B 504 TYR 0.015 0.001 TYR B 60 ARG 0.003 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 816) hydrogen bonds : angle 4.00316 ( 2373) covalent geometry : bond 0.00255 (14529) covalent geometry : angle 0.57282 (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 93 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: C 11 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.3784 (mmm160) REVERT: E 198 TRP cc_start: 0.7316 (p90) cc_final: 0.6969 (p90) REVERT: D 331 SER cc_start: 0.6570 (OUTLIER) cc_final: 0.6312 (t) outliers start: 15 outliers final: 12 residues processed: 90 average time/residue: 0.2009 time to fit residues: 30.6386 Evaluate side-chains 84 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 207 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 125 optimal weight: 0.0020 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 107 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- 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 69 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 = 0.4481 r_free = 0.4481 target = 0.085138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.074189 restraints weight = 108782.958| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 6.18 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14529 Z= 0.106 Angle : 0.572 8.511 20013 Z= 0.270 Chirality : 0.041 0.338 2543 Planarity : 0.004 0.085 2663 Dihedral : 3.551 29.051 2319 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 23.50 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2204 helix: 1.72 (0.16), residues: 1105 sheet: -1.19 (0.40), residues: 185 loop : -1.34 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 114 HIS 0.002 0.001 HIS C 149 PHE 0.012 0.001 PHE A 408 TYR 0.013 0.001 TYR B 60 ARG 0.005 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 816) hydrogen bonds : angle 3.98513 ( 2373) covalent geometry : bond 0.00251 (14529) covalent geometry : angle 0.57205 (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 84 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8916 (mm) cc_final: 0.8617 (tt) REVERT: C 11 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.4040 (mmm-85) REVERT: C 64 MET cc_start: 0.4899 (ttm) cc_final: 0.4554 (ttm) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.2036 time to fit residues: 28.2768 Evaluate side-chains 83 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 218 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 137 optimal weight: 0.0010 chunk 128 optimal weight: 0.0030 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 417 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.085009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.074059 restraints weight = 110158.287| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 6.21 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 14529 Z= 0.106 Angle : 0.563 8.204 20013 Z= 0.265 Chirality : 0.041 0.291 2543 Planarity : 0.004 0.085 2663 Dihedral : 3.494 27.951 2319 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 1.35 % Allowed : 23.40 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2204 helix: 1.80 (0.16), residues: 1105 sheet: -1.01 (0.39), residues: 192 loop : -1.26 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 7 HIS 0.002 0.000 HIS C 149 PHE 0.012 0.001 PHE B 466 TYR 0.012 0.001 TYR B 60 ARG 0.003 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.02586 ( 816) hydrogen bonds : angle 3.92740 ( 2373) covalent geometry : bond 0.00247 (14529) covalent geometry : angle 0.56324 (20013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7887.35 seconds wall clock time: 137 minutes 19.62 seconds (8239.62 seconds total)