Starting phenix.real_space_refine on Thu Sep 18 05:10:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yab_39094/09_2025/8yab_39094_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yab_39094/09_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_39094/09_2025/8yab_39094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yab_39094/09_2025/8yab_39094.map" model { file = "/net/cci-nas-00/data/ceres_data/8yab_39094/09_2025/8yab_39094_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yab_39094/09_2025/8yab_39094_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 13, 'GLU:plan': 34, 'HIS:plan': 10, 'GLN:plan1': 20, 'ARG:plan': 35, 'ASP:plan': 16, 'ASN:plan1': 3, 'TRP:plan': 4, 'TYR:plan': 5} 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: {'ASP:plan': 11, 'GLN:plan1': 13, 'ARG:plan': 21, 'PHE:plan': 3, 'GLU:plan': 17, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'HIS:plan': 3, 'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2} 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: {'GLU:plan': 13, 'ARG:plan': 6, 'ASP:plan': 14, 'GLN:plan1': 12, 'HIS:plan': 4, 'ASN:plan1': 7, 'TYR:plan': 6, 'PHE:plan': 4, 'TRP:plan': 1} 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: {'ARG:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 17, 'PHE:plan': 20, 'TRP:plan': 7, 'HIS:plan': 10, 'ASP:plan': 20, 'ASN:plan1': 15, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 605 Time building chain proxies: 3.46, per 1000 atoms: 0.24 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: 1.30 Conformation dependent library (CDL) restraints added in 679.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.64 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: 2.12 Time building geometry restraints manager: 1.54 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: 5.020 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG C 22 TYR 0.025 0.002 TYR B 368 PHE 0.018 0.002 PHE E 37 TRP 0.025 0.002 TRP C 114 HIS 0.008 0.002 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00961 (14529) covalent geometry : angle 1.15805 (20013) hydrogen bonds : bond 0.15949 ( 816) hydrogen bonds : angle 6.42562 ( 2373) *********************** 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 : 0.388 Fit side-chains revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7295 (ttp-170) cc_final: 0.6710 (tmm-80) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.0939 time to fit residues: 22.1280 Evaluate side-chains 88 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 216 optimal weight: 30.0000 chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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 130 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 = 0.4215 r_free = 0.4215 target = 0.092404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.079779 restraints weight = 81872.154| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 5.06 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14529 Z= 0.142 Angle : 0.684 15.136 20013 Z= 0.331 Chirality : 0.043 0.170 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.686 39.778 2328 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 20.91 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 2204 helix: 1.00 (0.16), residues: 1052 sheet: -1.16 (0.37), residues: 200 loop : -1.63 (0.22), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 59 TYR 0.014 0.001 TYR B 368 PHE 0.019 0.002 PHE E 51 TRP 0.013 0.001 TRP B 225 HIS 0.005 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00321 (14529) covalent geometry : angle 0.68415 (20013) hydrogen bonds : bond 0.03713 ( 816) hydrogen bonds : angle 4.82962 ( 2373) *********************** 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 124 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 583 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8199 (mp) REVERT: C 69 GLN cc_start: 0.7833 (mt0) cc_final: 0.7222 (mm110) REVERT: E 125 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 26 outliers final: 5 residues processed: 122 average time/residue: 0.0787 time to fit residues: 16.5492 Evaluate side-chains 91 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 236 THR 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 158 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 178 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 50.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.089737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.076899 restraints weight = 83485.264| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.03 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14529 Z= 0.169 Angle : 0.631 11.415 20013 Z= 0.309 Chirality : 0.043 0.232 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.486 30.792 2321 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 3.42 % Allowed : 21.01 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 2204 helix: 1.06 (0.16), residues: 1074 sheet: -0.78 (0.37), residues: 195 loop : -1.73 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 59 TYR 0.015 0.002 TYR B 368 PHE 0.016 0.002 PHE E 51 TRP 0.011 0.001 TRP B 291 HIS 0.006 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00390 (14529) covalent geometry : angle 0.63077 (20013) hydrogen bonds : bond 0.03780 ( 816) hydrogen bonds : angle 4.61034 ( 2373) *********************** 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: 33 poor density : 89 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 GLN cc_start: 0.7943 (mt0) cc_final: 0.7241 (mm110) REVERT: E 125 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8252 (mp) outliers start: 33 outliers final: 13 residues processed: 118 average time/residue: 0.0757 time to fit residues: 15.5156 Evaluate side-chains 92 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain E residue 32 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 0.0020 chunk 145 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 112 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 175 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 186 optimal weight: 0.0970 overall best weight: 0.1398 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.092085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.079395 restraints weight = 82883.045| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 5.09 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 14529 Z= 0.109 Angle : 0.584 11.114 20013 Z= 0.279 Chirality : 0.042 0.441 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.970 27.953 2319 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 3.11 % Allowed : 21.43 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 2204 helix: 1.34 (0.16), residues: 1078 sheet: -0.74 (0.37), residues: 196 loop : -1.61 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 549 TYR 0.012 0.001 TYR A 654 PHE 0.019 0.001 PHE E 51 TRP 0.026 0.001 TRP A 442 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00250 (14529) covalent geometry : angle 0.58447 (20013) hydrogen bonds : bond 0.02887 ( 816) hydrogen bonds : angle 4.27093 ( 2373) *********************** 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 125 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: B 583 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7905 (mp) REVERT: C 69 GLN cc_start: 0.7823 (mt0) cc_final: 0.7068 (mm110) REVERT: C 134 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6851 (mt) REVERT: E 125 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 335 ASP cc_start: 0.8266 (t0) cc_final: 0.8050 (t0) outliers start: 30 outliers final: 5 residues processed: 123 average time/residue: 0.0733 time to fit residues: 15.9735 Evaluate side-chains 90 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 63 SER 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 390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 223 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 131 optimal weight: 0.0070 chunk 144 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.088298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.075324 restraints weight = 83956.863| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 5.05 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14529 Z= 0.190 Angle : 0.642 10.627 20013 Z= 0.316 Chirality : 0.043 0.197 2543 Planarity : 0.005 0.079 2663 Dihedral : 4.247 30.112 2319 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.17 % Favored : 93.69 % Rotamer: Outliers : 2.69 % Allowed : 23.08 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.19), residues: 2204 helix: 1.28 (0.16), residues: 1088 sheet: -0.84 (0.37), residues: 197 loop : -1.64 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.015 0.002 TYR E 27 PHE 0.017 0.002 PHE A 565 TRP 0.016 0.002 TRP B 291 HIS 0.007 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00434 (14529) covalent geometry : angle 0.64199 (20013) hydrogen bonds : bond 0.03669 ( 816) hydrogen bonds : angle 4.46531 ( 2373) *********************** 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: 26 poor density : 81 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: B 583 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8311 (mp) REVERT: C 69 GLN cc_start: 0.7871 (mt0) cc_final: 0.7112 (mm110) REVERT: C 150 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (tt) REVERT: C 170 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9164 (mp) REVERT: C 180 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.4011 (mt) REVERT: D 335 ASP cc_start: 0.8556 (t0) cc_final: 0.8339 (t0) outliers start: 26 outliers final: 15 residues processed: 104 average time/residue: 0.0808 time to fit residues: 14.6441 Evaluate side-chains 92 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 505 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 chunk 190 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.088283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075448 restraints weight = 84045.301| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.02 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2618 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= 0.152 Angle : 0.609 10.690 20013 Z= 0.295 Chirality : 0.042 0.177 2543 Planarity : 0.005 0.079 2663 Dihedral : 4.139 29.512 2319 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer: Outliers : 3.31 % Allowed : 23.19 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 2204 helix: 1.36 (0.16), residues: 1082 sheet: -0.94 (0.37), residues: 197 loop : -1.60 (0.22), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.012 0.001 TYR E 27 PHE 0.016 0.002 PHE C 29 TRP 0.013 0.001 TRP B 291 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00355 (14529) covalent geometry : angle 0.60887 (20013) hydrogen bonds : bond 0.03300 ( 816) hydrogen bonds : angle 4.35378 ( 2373) *********************** 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 111 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 564 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6349 (t80) REVERT: B 583 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 69 GLN cc_start: 0.7827 (mt0) cc_final: 0.7203 (mm110) REVERT: C 150 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7989 (tt) REVERT: C 170 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9208 (mp) REVERT: C 180 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.4053 (mt) REVERT: D 335 ASP cc_start: 0.8548 (t0) cc_final: 0.8331 (t0) outliers start: 32 outliers final: 16 residues processed: 106 average time/residue: 0.0843 time to fit residues: 15.4533 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 448 THR 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 A residue 564 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 171 optimal weight: 10.0000 chunk 196 optimal weight: 40.0000 chunk 148 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 205 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 621 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.085284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.072295 restraints weight = 85232.270| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 5.01 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14529 Z= 0.268 Angle : 0.721 11.247 20013 Z= 0.359 Chirality : 0.045 0.174 2543 Planarity : 0.005 0.082 2663 Dihedral : 4.789 32.551 2319 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.67 % Favored : 92.20 % Rotamer: Outliers : 3.83 % Allowed : 23.29 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.19), residues: 2204 helix: 0.89 (0.16), residues: 1097 sheet: -1.03 (0.39), residues: 177 loop : -1.81 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 363 TYR 0.019 0.002 TYR E 326 PHE 0.021 0.002 PHE C 29 TRP 0.015 0.002 TRP E 231 HIS 0.012 0.002 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00601 (14529) covalent geometry : angle 0.72054 (20013) hydrogen bonds : bond 0.04357 ( 816) hydrogen bonds : angle 4.85175 ( 2373) *********************** 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 104 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.548 Fit side-chains REVERT: A 564 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6440 (t80) REVERT: B 583 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 68 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: C 150 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (tt) REVERT: C 170 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9204 (mp) REVERT: C 180 LEU cc_start: 0.4901 (OUTLIER) cc_final: 0.4452 (mt) REVERT: E 313 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5518 (p90) outliers start: 37 outliers final: 25 residues processed: 99 average time/residue: 0.0776 time to fit residues: 13.7511 Evaluate side-chains 96 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain B residue 289 LEU 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 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 153 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 194 optimal weight: 40.0000 chunk 195 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.086222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.073388 restraints weight = 84632.900| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 4.94 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14529 Z= 0.179 Angle : 0.642 10.857 20013 Z= 0.314 Chirality : 0.043 0.217 2543 Planarity : 0.005 0.082 2663 Dihedral : 4.501 32.799 2319 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 3.42 % Allowed : 24.43 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.19), residues: 2204 helix: 1.06 (0.16), residues: 1095 sheet: -1.19 (0.38), residues: 180 loop : -1.76 (0.22), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.014 0.002 TYR E 326 PHE 0.017 0.002 PHE C 29 TRP 0.012 0.001 TRP E 231 HIS 0.006 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00414 (14529) covalent geometry : angle 0.64222 (20013) hydrogen bonds : bond 0.03540 ( 816) hydrogen bonds : angle 4.57428 ( 2373) *********************** 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 98 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.557 Fit side-chains REVERT: A 564 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6390 (t80) REVERT: B 583 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 69 GLN cc_start: 0.7899 (mt0) cc_final: 0.7218 (mm110) REVERT: C 170 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9234 (mp) REVERT: C 180 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.4325 (mt) REVERT: E 313 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.5483 (p90) outliers start: 33 outliers final: 22 residues processed: 94 average time/residue: 0.0767 time to fit residues: 13.1322 Evaluate side-chains 91 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 448 THR 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 A residue 564 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 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 252 ILE Chi-restraints excluded: chain E residue 313 TYR 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 22 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 191 optimal weight: 0.0270 chunk 165 optimal weight: 2.9990 overall best weight: 1.0640 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.087714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075023 restraints weight = 84473.489| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.95 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14529 Z= 0.118 Angle : 0.600 10.375 20013 Z= 0.286 Chirality : 0.041 0.196 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.112 31.987 2319 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.08 % Favored : 94.78 % Rotamer: Outliers : 2.38 % Allowed : 25.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 2204 helix: 1.35 (0.16), residues: 1097 sheet: -1.10 (0.38), residues: 183 loop : -1.63 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.011 0.001 TYR B 368 PHE 0.028 0.001 PHE A 565 TRP 0.013 0.001 TRP B 291 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00276 (14529) covalent geometry : angle 0.60033 (20013) hydrogen bonds : bond 0.02969 ( 816) hydrogen bonds : angle 4.25111 ( 2373) *********************** 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: 23 poor density : 70 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7589 (ptt180) REVERT: B 583 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 69 GLN cc_start: 0.7851 (mt0) cc_final: 0.7206 (mm110) REVERT: C 180 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4065 (mt) outliers start: 23 outliers final: 14 residues processed: 90 average time/residue: 0.0808 time to fit residues: 12.9228 Evaluate side-chains 86 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 544 MET 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 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 252 ILE 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 212 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 163 optimal weight: 0.1980 chunk 47 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 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 = 0.4163 r_free = 0.4163 target = 0.088333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.075757 restraints weight = 83850.161| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.93 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14529 Z= 0.108 Angle : 0.593 11.158 20013 Z= 0.280 Chirality : 0.041 0.176 2543 Planarity : 0.005 0.079 2663 Dihedral : 3.872 30.961 2319 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 2.28 % Allowed : 25.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 2204 helix: 1.53 (0.16), residues: 1100 sheet: -1.07 (0.37), residues: 197 loop : -1.57 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.016 0.001 TYR E 313 PHE 0.015 0.001 PHE E 51 TRP 0.013 0.001 TRP B 291 HIS 0.003 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00257 (14529) covalent geometry : angle 0.59289 (20013) hydrogen bonds : bond 0.02751 ( 816) hydrogen bonds : angle 4.08576 ( 2373) ********************** 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 98 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 728 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7741 (ptt180) REVERT: C 69 GLN cc_start: 0.7808 (mt0) cc_final: 0.7283 (mm110) REVERT: C 150 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (tt) REVERT: C 180 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4044 (mt) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.0815 time to fit residues: 13.4748 Evaluate side-chains 88 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 544 MET Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 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 252 ILE 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 174 optimal weight: 0.0670 chunk 145 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 ** 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 = 0.4163 r_free = 0.4163 target = 0.088295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.075746 restraints weight = 83519.109| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.94 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14529 Z= 0.109 Angle : 0.592 11.033 20013 Z= 0.278 Chirality : 0.041 0.181 2543 Planarity : 0.005 0.078 2663 Dihedral : 3.780 30.360 2319 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 2.07 % Allowed : 25.57 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.19), residues: 2204 helix: 1.64 (0.16), residues: 1102 sheet: -1.13 (0.38), residues: 198 loop : -1.55 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 59 TYR 0.010 0.001 TYR B 368 PHE 0.014 0.001 PHE E 51 TRP 0.013 0.001 TRP B 291 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00260 (14529) covalent geometry : angle 0.59157 (20013) hydrogen bonds : bond 0.02709 ( 816) hydrogen bonds : angle 4.03545 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.95 seconds wall clock time: 52 minutes 27.33 seconds (3147.33 seconds total)