Starting phenix.real_space_refine on Tue Nov 18 12:59:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yah_39099/11_2025/8yah_39099.map" } resolution = 3.3 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 9022 2.51 5 N 2605 2.21 5 O 2638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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: 3.69, per 1000 atoms: 0.26 Number of scatterers: 14309 At special positions: 0 Unit cell: (117.3, 126.65, 164.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2638 8.00 N 2605 7.00 C 9022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 698.3 milliseconds 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: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.742A pdb=" N VAL A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.791A pdb=" N VAL A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.963A pdb=" N ALA A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 4.262A pdb=" N LYS A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.611A pdb=" N CYS A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.630A pdb=" N GLN A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.628A pdb=" N CYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.750A pdb=" N VAL A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 354 removed outlier: 4.384A pdb=" N TYR A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.533A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.588A pdb=" N ASN A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 443 removed outlier: 3.656A pdb=" N LYS A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 removed outlier: 5.127A pdb=" N VAL A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 463 through 473 removed outlier: 4.599A pdb=" N HIS A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.748A pdb=" N GLN A 516 " --> pdb=" O PRO A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.743A pdb=" N GLU A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.541A pdb=" N LEU A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.053A pdb=" N GLY A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 623 through 633 Processing helix chain 'A' and resid 633 through 640 removed outlier: 4.148A pdb=" N ILE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 664 through 683 removed outlier: 4.128A pdb=" N ILE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 710 removed outlier: 3.635A pdb=" N VAL A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 3.546A pdb=" N ARG A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.394A pdb=" N ALA A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 761 removed outlier: 4.444A pdb=" N LEU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.590A pdb=" N ALA A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 768 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.940A pdb=" N ALA B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.592A pdb=" N GLU B 30 " --> pdb=" O PRO B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 31 through 39 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.661A pdb=" N GLY B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 181 through 204 removed outlier: 3.538A pdb=" N LEU B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 278 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 304 through 307 removed outlier: 3.744A pdb=" N LEU B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.751A pdb=" N HIS B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.825A pdb=" N LEU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.670A pdb=" N LEU B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 454 removed outlier: 3.520A pdb=" N LEU B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 497 Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.629A pdb=" N PHE B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 530 Proline residue: B 518 - end of helix removed outlier: 4.041A pdb=" N ARG B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 548 removed outlier: 4.468A pdb=" N GLN B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET B 543 " --> pdb=" O TRP B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.950A pdb=" N THR B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 removed outlier: 4.073A pdb=" N LEU B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 removed outlier: 4.153A pdb=" N GLN B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 622 Processing helix chain 'B' and resid 623 through 630 removed outlier: 3.810A pdb=" N GLY B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 71 removed outlier: 4.179A pdb=" N ILE C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.631A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 removed outlier: 4.142A pdb=" N ILE C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'E' and resid 27 through 39 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 47 through 59 Processing helix chain 'E' and resid 125 through 143 removed outlier: 4.438A pdb=" N SER E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.129A pdb=" N GLN E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.767A pdb=" N LEU E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 276 through 282 Processing helix chain 'E' and resid 484 through 489 removed outlier: 4.420A pdb=" N LEU E 488 " --> pdb=" O THR E 484 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 489 " --> pdb=" O TYR E 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 484 through 489' Processing helix chain 'D' and resid 34 through 39 removed outlier: 3.573A pdb=" N MET D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.708A pdb=" N GLY D 123 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 144 Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.873A pdb=" N ASP D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 317 through 328 removed outlier: 4.144A pdb=" N TYR D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 352 removed outlier: 4.020A pdb=" N SER D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.647A pdb=" N ASP D 365 " --> pdb=" O TRP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 509 Processing helix chain 'D' and resid 510 through 520 removed outlier: 4.192A pdb=" N VAL D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 28 removed outlier: 3.780A pdb=" N ALA C 4 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 123 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 8 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 117 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 122 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 114 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 96 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.828A pdb=" N PHE C 106 " --> pdb=" O ALA C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 21 through 26 removed outlier: 6.309A pdb=" N LEU E 8 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER E 24 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 6 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARG E 26 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ARG E 4 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 5 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 107 " --> pdb=" O TRP E 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'E' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'E' and resid 216 through 220 Processing sheet with id=AA7, first strand: chain 'E' and resid 253 through 254 removed outlier: 3.563A pdb=" N SER E 253 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 322 through 325 removed outlier: 3.625A pdb=" N ASN E 340 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 328 through 330 removed outlier: 4.057A pdb=" N LYS E 329 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 336 " --> pdb=" O LYS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 356 through 357 removed outlier: 3.737A pdb=" N ILE E 430 " --> pdb=" O ILE E 474 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 474 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 369 through 370 removed outlier: 3.946A pdb=" N GLU E 370 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 77 through 80 removed outlier: 3.531A pdb=" N GLY D 55 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA D 45 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER D 475 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 47 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 88 removed outlier: 4.188A pdb=" N HIS D 86 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 105 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU D 117 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE D 129 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN D 119 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA D 127 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 154 through 160 removed outlier: 6.434A pdb=" N ILE D 156 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE D 167 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 158 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 165 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 173 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE D 191 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN D 189 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 207 removed outlier: 6.409A pdb=" N LEU D 216 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR D 206 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE D 214 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 215 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.674A pdb=" N ALA D 271 " --> pdb=" O LEU D 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 280 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 428 through 432 removed outlier: 5.242A pdb=" N CYS D 429 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR D 440 " --> pdb=" O CYS D 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 481 through 484 removed outlier: 3.845A pdb=" N CYS D 481 " --> pdb=" O ILE D 492 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 10 1.17 - 1.33: 3279 1.33 - 1.49: 5206 1.49 - 1.65: 5981 1.65 - 1.81: 53 Bond restraints: 14529 Sorted by residual: bond pdb=" CG PRO E 482 " pdb=" CD PRO E 482 " ideal model delta sigma weight residual 1.503 1.084 0.419 3.40e-02 8.65e+02 1.52e+02 bond pdb=" CA ARG C 22 " pdb=" C ARG C 22 " ideal model delta sigma weight residual 1.523 1.390 0.133 1.23e-02 6.61e+03 1.17e+02 bond pdb=" CG PRO B 437 " pdb=" CD PRO B 437 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+02 bond pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 1.492 1.009 0.483 5.00e-02 4.00e+02 9.35e+01 bond pdb=" C TYR D 323 " pdb=" O TYR D 323 " ideal model delta sigma weight residual 1.236 1.112 0.124 1.29e-02 6.01e+03 9.25e+01 ... (remaining 14524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.38: 19998 13.38 - 26.75: 9 26.75 - 40.13: 5 40.13 - 53.50: 0 53.50 - 66.88: 1 Bond angle restraints: 20013 Sorted by residual: angle pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " pdb=" CD PRO B 376 " ideal model delta sigma weight residual 106.10 172.98 -66.88 3.20e+00 9.77e-02 4.37e+02 angle pdb=" N PRO B 437 " pdb=" CD PRO B 437 " pdb=" CG PRO B 437 " ideal model delta sigma weight residual 103.20 72.38 30.82 1.50e+00 4.44e-01 4.22e+02 angle pdb=" CA PRO B 437 " pdb=" CB PRO B 437 " pdb=" CG PRO B 437 " ideal model delta sigma weight residual 104.50 67.10 37.40 1.90e+00 2.77e-01 3.87e+02 angle pdb=" N PRO B 376 " pdb=" CD PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 103.20 76.05 27.15 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CA PRO B 376 " pdb=" CB PRO B 376 " pdb=" CG PRO B 376 " ideal model delta sigma weight residual 104.50 73.70 30.80 1.90e+00 2.77e-01 2.63e+02 ... (remaining 20008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 7815 16.00 - 32.01: 619 32.01 - 48.01: 163 48.01 - 64.02: 33 64.02 - 80.02: 12 Dihedral angle restraints: 8642 sinusoidal: 2073 harmonic: 6569 Sorted by residual: dihedral pdb=" C ARG D 336 " pdb=" N ARG D 336 " pdb=" CA ARG D 336 " pdb=" CB ARG D 336 " ideal model delta harmonic sigma weight residual -122.60 -140.86 18.26 0 2.50e+00 1.60e-01 5.34e+01 dihedral pdb=" C PHE D 332 " pdb=" N PHE D 332 " pdb=" CA PHE D 332 " pdb=" CB PHE D 332 " ideal model delta harmonic sigma weight residual -122.60 -140.13 17.53 0 2.50e+00 1.60e-01 4.92e+01 dihedral pdb=" N PHE D 332 " pdb=" C PHE D 332 " pdb=" CA PHE D 332 " pdb=" CB PHE D 332 " ideal model delta harmonic sigma weight residual 122.80 139.52 -16.72 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 2532 0.197 - 0.393: 4 0.393 - 0.590: 4 0.590 - 0.786: 2 0.786 - 0.983: 1 Chirality restraints: 2543 Sorted by residual: chirality pdb=" CA ARG D 336 " pdb=" N ARG D 336 " pdb=" C ARG D 336 " pdb=" CB ARG D 336 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA PHE D 332 " pdb=" N PHE D 332 " pdb=" C PHE D 332 " pdb=" CB PHE D 332 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA SER D 331 " pdb=" N SER D 331 " pdb=" C SER D 331 " pdb=" CB SER D 331 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 2540 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 22 " -0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C ARG C 22 " 0.094 2.00e-02 2.50e+03 pdb=" O ARG C 22 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL C 23 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 481 " -0.072 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO E 482 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 482 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 482 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 336 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ARG D 336 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG D 336 " -0.022 2.00e-02 2.50e+03 pdb=" N SER D 337 " -0.019 2.00e-02 2.50e+03 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 12 2.20 - 2.87: 5492 2.87 - 3.55: 20472 3.55 - 4.22: 28787 4.22 - 4.90: 49657 Nonbonded interactions: 104420 Sorted by model distance: nonbonded pdb=" CD2 LEU C 48 " pdb=" CB TYR D 323 " model vdw 1.522 3.860 nonbonded pdb=" O GLU C 103 " pdb=" O PHE D 332 " model vdw 1.779 3.040 nonbonded pdb=" CB LEU C 49 " pdb=" CD1 LEU D 327 " model vdw 1.801 3.860 nonbonded pdb=" NH2 ARG C 59 " pdb=" N ASP D 316 " model vdw 2.120 3.200 nonbonded pdb=" CG LEU C 49 " pdb=" CD1 LEU D 327 " model vdw 2.121 3.890 ... (remaining 104415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.483 14529 Z= 0.404 Angle : 1.159 66.876 20013 Z= 0.593 Chirality : 0.058 0.983 2543 Planarity : 0.007 0.101 2663 Dihedral : 13.954 80.023 4336 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.85 % Favored : 91.70 % Rotamer: Outliers : 0.72 % Allowed : 20.08 % Favored : 79.19 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2204 helix: 0.55 (0.16), residues: 1045 sheet: -1.23 (0.39), residues: 178 loop : -1.89 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 22 TYR 0.025 0.003 TYR B 368 PHE 0.018 0.002 PHE E 37 TRP 0.024 0.002 TRP C 114 HIS 0.008 0.002 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00962 (14529) covalent geometry : angle 1.15856 (20013) hydrogen bonds : bond 0.15949 ( 816) hydrogen bonds : angle 6.42626 ( 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 150 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 SER cc_start: -0.3514 (OUTLIER) cc_final: -0.4280 (p) REVERT: C 5 PHE cc_start: 0.4190 (t80) cc_final: 0.3878 (t80) outliers start: 7 outliers final: 3 residues processed: 150 average time/residue: 0.1189 time to fit residues: 27.1830 Evaluate side-chains 90 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain D residue 318 PRO Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 337 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.095617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.084908 restraints weight = 107281.665| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 6.57 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14529 Z= 0.140 Angle : 0.698 16.626 20013 Z= 0.336 Chirality : 0.043 0.221 2543 Planarity : 0.005 0.080 2663 Dihedral : 4.589 38.234 2326 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 2.48 % Allowed : 19.25 % Favored : 78.26 % 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 are not related in a simple way. whole: -0.55 (0.19), residues: 2204 helix: 0.89 (0.16), residues: 1078 sheet: -1.19 (0.38), residues: 184 loop : -1.69 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 59 TYR 0.013 0.001 TYR A 654 PHE 0.020 0.002 PHE E 51 TRP 0.013 0.001 TRP B 225 HIS 0.005 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00327 (14529) covalent geometry : angle 0.69794 (20013) hydrogen bonds : bond 0.03712 ( 816) hydrogen bonds : angle 4.84284 ( 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 120 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8966 (mm) cc_final: 0.8654 (mm) REVERT: B 343 ASP cc_start: 0.8863 (t0) cc_final: 0.8645 (t0) REVERT: B 515 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8331 (tp) REVERT: E 80 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6969 (ptmm) outliers start: 24 outliers final: 5 residues processed: 116 average time/residue: 0.0902 time to fit residues: 17.3680 Evaluate side-chains 89 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 158 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 98 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 552 GLN B 183 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.088964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.077701 restraints weight = 109501.801| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 6.40 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14529 Z= 0.218 Angle : 0.728 11.732 20013 Z= 0.366 Chirality : 0.045 0.266 2543 Planarity : 0.006 0.082 2663 Dihedral : 4.745 30.833 2319 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.76 % Favored : 93.10 % Rotamer: Outliers : 3.93 % Allowed : 18.94 % Favored : 77.12 % 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 are not related in a simple way. whole: -0.70 (0.19), residues: 2204 helix: 0.74 (0.16), residues: 1083 sheet: -1.56 (0.36), residues: 197 loop : -1.66 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 549 TYR 0.024 0.002 TYR E 27 PHE 0.029 0.003 PHE C 29 TRP 0.069 0.003 TRP B 65 HIS 0.005 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00495 (14529) covalent geometry : angle 0.72845 (20013) hydrogen bonds : bond 0.04572 ( 816) hydrogen bonds : angle 4.88252 ( 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 120 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 343 ASP cc_start: 0.8957 (t0) cc_final: 0.8752 (t0) REVERT: B 471 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8419 (mt) REVERT: E 80 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6745 (ptmm) REVERT: E 198 TRP cc_start: 0.7586 (p90) cc_final: 0.7336 (p90) outliers start: 38 outliers final: 17 residues processed: 113 average time/residue: 0.0876 time to fit residues: 16.9342 Evaluate side-chains 94 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 61 optimal weight: 0.9990 chunk 158 optimal weight: 0.0470 chunk 145 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 112 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 552 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.089799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.078631 restraints weight = 108622.058| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 6.36 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14529 Z= 0.115 Angle : 0.596 11.973 20013 Z= 0.286 Chirality : 0.042 0.400 2543 Planarity : 0.005 0.082 2663 Dihedral : 4.017 28.841 2319 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.28 % Rotamer: Outliers : 3.00 % Allowed : 19.46 % Favored : 77.54 % 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 are not related in a simple way. whole: -0.18 (0.19), residues: 2204 helix: 1.27 (0.16), residues: 1083 sheet: -1.39 (0.37), residues: 185 loop : -1.53 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 268 TYR 0.009 0.001 TYR A 654 PHE 0.019 0.002 PHE E 51 TRP 0.018 0.002 TRP B 65 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00264 (14529) covalent geometry : angle 0.59617 (20013) hydrogen bonds : bond 0.03066 ( 816) hydrogen bonds : angle 4.34046 ( 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 112 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9013 (mm) cc_final: 0.8713 (mm) REVERT: B 343 ASP cc_start: 0.8977 (t0) cc_final: 0.8703 (t0) REVERT: B 543 MET cc_start: 0.7524 (mmm) cc_final: 0.7308 (tpp) REVERT: E 198 TRP cc_start: 0.7484 (p90) cc_final: 0.7173 (p90) outliers start: 29 outliers final: 14 residues processed: 107 average time/residue: 0.0951 time to fit residues: 17.0483 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 223 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 224 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 49 optimal weight: 0.0050 chunk 10 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.088988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.077856 restraints weight = 108838.712| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 6.36 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14529 Z= 0.117 Angle : 0.580 10.340 20013 Z= 0.276 Chirality : 0.041 0.275 2543 Planarity : 0.005 0.081 2663 Dihedral : 3.792 28.446 2319 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 19.46 % Favored : 77.85 % 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 are not related in a simple way. whole: 0.10 (0.19), residues: 2204 helix: 1.52 (0.16), residues: 1090 sheet: -1.27 (0.38), residues: 185 loop : -1.45 (0.22), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 268 TYR 0.010 0.001 TYR E 27 PHE 0.016 0.001 PHE A 565 TRP 0.007 0.001 TRP E 198 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00269 (14529) covalent geometry : angle 0.58043 (20013) hydrogen bonds : bond 0.02900 ( 816) hydrogen bonds : angle 4.09639 ( 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 106 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9031 (mm) cc_final: 0.8724 (mm) REVERT: E 198 TRP cc_start: 0.7483 (p90) cc_final: 0.7180 (p90) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.0844 time to fit residues: 14.6394 Evaluate side-chains 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 137 optimal weight: 0.0050 chunk 157 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.085817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.074645 restraints weight = 109723.096| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 6.25 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14529 Z= 0.154 Angle : 0.642 10.341 20013 Z= 0.311 Chirality : 0.042 0.181 2543 Planarity : 0.005 0.081 2663 Dihedral : 4.140 29.096 2319 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 3.31 % Allowed : 20.08 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2204 helix: 1.33 (0.16), residues: 1092 sheet: -1.31 (0.38), residues: 185 loop : -1.54 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 268 TYR 0.016 0.002 TYR E 27 PHE 0.022 0.002 PHE B 466 TRP 0.041 0.002 TRP B 223 HIS 0.004 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00343 (14529) covalent geometry : angle 0.64189 (20013) hydrogen bonds : bond 0.03598 ( 816) hydrogen bonds : angle 4.27902 ( 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 110 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9045 (mm) cc_final: 0.8741 (mm) outliers start: 32 outliers final: 21 residues processed: 103 average time/residue: 0.0850 time to fit residues: 15.1569 Evaluate side-chains 93 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 171 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 148 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- 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** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.084019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.072865 restraints weight = 109556.224| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 6.24 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14529 Z= 0.178 Angle : 0.652 10.603 20013 Z= 0.317 Chirality : 0.044 0.337 2543 Planarity : 0.005 0.083 2663 Dihedral : 4.287 29.907 2319 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 3.11 % Allowed : 21.22 % Favored : 75.67 % 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 are not related in a simple way. whole: -0.27 (0.19), residues: 2204 helix: 1.17 (0.16), residues: 1102 sheet: -1.48 (0.38), residues: 188 loop : -1.60 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.022 0.002 TYR B 60 PHE 0.025 0.002 PHE A 451 TRP 0.025 0.002 TRP B 295 HIS 0.004 0.001 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00404 (14529) covalent geometry : angle 0.65170 (20013) hydrogen bonds : bond 0.03628 ( 816) hydrogen bonds : angle 4.47082 ( 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 101 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9054 (mm) cc_final: 0.8785 (mm) REVERT: E 179 ASN cc_start: 0.7014 (OUTLIER) cc_final: 0.6632 (m-40) outliers start: 30 outliers final: 18 residues processed: 95 average time/residue: 0.0794 time to fit residues: 13.6197 Evaluate side-chains 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 153 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 27 optimal weight: 0.0570 chunk 91 optimal weight: 0.0000 chunk 173 optimal weight: 0.0570 chunk 194 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 overall best weight: 0.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.085486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.074448 restraints weight = 108793.841| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 6.25 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14529 Z= 0.110 Angle : 0.595 11.747 20013 Z= 0.280 Chirality : 0.042 0.283 2543 Planarity : 0.004 0.082 2663 Dihedral : 3.804 29.698 2319 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 1.66 % Allowed : 22.67 % Favored : 75.67 % 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 are not related in a simple way. whole: 0.13 (0.19), residues: 2204 helix: 1.55 (0.16), residues: 1099 sheet: -1.54 (0.37), residues: 203 loop : -1.39 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.014 0.001 TYR B 60 PHE 0.015 0.001 PHE E 51 TRP 0.015 0.001 TRP E 7 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00257 (14529) covalent geometry : angle 0.59536 (20013) hydrogen bonds : bond 0.02795 ( 816) hydrogen bonds : angle 4.09255 ( 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 86 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8985 (mm) cc_final: 0.8759 (mm) REVERT: E 179 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6597 (m-40) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.0809 time to fit residues: 12.1565 Evaluate side-chains 81 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 22 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 184 optimal weight: 0.0670 chunk 186 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 191 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.084166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.073084 restraints weight = 110011.555| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 6.20 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14529 Z= 0.133 Angle : 0.608 10.729 20013 Z= 0.288 Chirality : 0.042 0.261 2543 Planarity : 0.005 0.084 2663 Dihedral : 3.848 28.365 2319 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 1.66 % Allowed : 22.88 % 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 are not related in a simple way. whole: 0.16 (0.19), residues: 2204 helix: 1.55 (0.16), residues: 1106 sheet: -1.20 (0.40), residues: 178 loop : -1.45 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 549 TYR 0.014 0.001 TYR B 60 PHE 0.017 0.002 PHE B 466 TRP 0.016 0.001 TRP B 295 HIS 0.003 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00309 (14529) covalent geometry : angle 0.60845 (20013) hydrogen bonds : bond 0.03104 ( 816) hydrogen bonds : angle 4.14926 ( 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 87 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9045 (mm) cc_final: 0.8819 (mm) REVERT: E 179 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6511 (m-40) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.0901 time to fit residues: 12.7672 Evaluate side-chains 81 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 212 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.084083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.073054 restraints weight = 109083.562| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 6.18 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14529 Z= 0.124 Angle : 0.604 10.869 20013 Z= 0.284 Chirality : 0.042 0.244 2543 Planarity : 0.005 0.083 2663 Dihedral : 3.799 29.361 2319 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 1.45 % Allowed : 23.60 % Favored : 74.95 % 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 are not related in a simple way. whole: 0.22 (0.19), residues: 2204 helix: 1.57 (0.16), residues: 1112 sheet: -1.37 (0.40), residues: 180 loop : -1.34 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 28 TYR 0.015 0.001 TYR B 60 PHE 0.015 0.001 PHE A 408 TRP 0.011 0.001 TRP A 442 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00292 (14529) covalent geometry : angle 0.60433 (20013) hydrogen bonds : bond 0.02952 ( 816) hydrogen bonds : angle 4.07903 ( 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 81 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9054 (mm) cc_final: 0.8852 (mm) REVERT: E 179 ASN cc_start: 0.6944 (OUTLIER) cc_final: 0.6517 (m-40) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.0812 time to fit residues: 11.7469 Evaluate side-chains 78 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 174 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 204 optimal weight: 0.3980 chunk 144 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.084098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.073086 restraints weight = 108678.815| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 6.19 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14529 Z= 0.116 Angle : 0.587 10.602 20013 Z= 0.275 Chirality : 0.042 0.237 2543 Planarity : 0.004 0.083 2663 Dihedral : 3.664 28.731 2319 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 1.55 % Allowed : 23.50 % Favored : 74.95 % 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 are not related in a simple way. whole: 0.38 (0.19), residues: 2204 helix: 1.69 (0.16), residues: 1109 sheet: -1.14 (0.39), residues: 192 loop : -1.28 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 549 TYR 0.014 0.001 TYR B 60 PHE 0.014 0.001 PHE B 466 TRP 0.011 0.001 TRP E 7 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00274 (14529) covalent geometry : angle 0.58738 (20013) hydrogen bonds : bond 0.02817 ( 816) hydrogen bonds : angle 4.00496 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3991.22 seconds wall clock time: 68 minutes 53.24 seconds (4133.24 seconds total)