Starting phenix.real_space_refine on Thu Jul 31 14:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.map" model { file = "/net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdj_16575/07_2025/8cdj_16575.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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 68 5.16 5 C 8607 2.51 5 N 2391 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13623 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5185 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 11, 'TRANS': 690} Chain breaks: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 721 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 365 Chain: "R" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 5968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 5968 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 38, 'TRANS': 804} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 28, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 330 Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 1612 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 906 Unresolved non-hydrogen angles: 1167 Unresolved non-hydrogen dihedrals: 736 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 4, 'ASP:plan': 16, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 470 Chain: "S" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 768 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 Time building chain proxies: 10.25, per 1000 atoms: 0.75 Number of scatterers: 13623 At special positions: 0 Unit cell: (157.472, 144.704, 120.87, 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 68 16.00 O 2557 8.00 N 2391 7.00 C 8607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 2.7 seconds 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3852 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 8 sheets defined 73.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'C' and resid 17 through 33 removed outlier: 4.316A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 87 through 108 removed outlier: 3.639A pdb=" N ASN C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 99 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 137 removed outlier: 4.072A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 removed outlier: 4.216A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS C 143 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 192 removed outlier: 3.595A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 4.380A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.822A pdb=" N GLU C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 255 removed outlier: 3.613A pdb=" N ARG C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.583A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.728A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.858A pdb=" N ARG C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 356 removed outlier: 3.918A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 4.302A pdb=" N ASN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.737A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.889A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.545A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 455 removed outlier: 3.554A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 4.230A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.645A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 525 removed outlier: 3.715A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.974A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.697A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 642 " --> pdb=" O GLN C 638 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 722 removed outlier: 3.890A pdb=" N LYS C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET C 721 " --> pdb=" O ARG C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 44 through 56 removed outlier: 4.183A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.706A pdb=" N GLN D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.910A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.536A pdb=" N LYS D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.529A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.533A pdb=" N LEU D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 170 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN D 171 " --> pdb=" O LEU D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 171' Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.703A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.756A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.607A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 4.186A pdb=" N GLU D 251 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 Proline residue: D 258 - end of helix removed outlier: 3.560A pdb=" N CYS D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.654A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.938A pdb=" N TYR D 291 " --> pdb=" O PRO D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 345 through 362 removed outlier: 4.173A pdb=" N VAL D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.589A pdb=" N SER D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Proline residue: D 377 - end of helix Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.554A pdb=" N LYS D 391 " --> pdb=" O GLU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 4.129A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.676A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 453 " --> pdb=" O LYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.556A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.589A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 548 " --> pdb=" O GLN D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.750A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 600 Processing helix chain 'D' and resid 604 through 606 No H-bonds generated for 'chain 'D' and resid 604 through 606' Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.561A pdb=" N THR D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 619 " --> pdb=" O PHE D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 636 Processing helix chain 'D' and resid 644 through 658 removed outlier: 3.761A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Proline residue: D 653 - end of helix removed outlier: 3.598A pdb=" N PHE D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 681 removed outlier: 3.636A pdb=" N LEU D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 701 removed outlier: 3.655A pdb=" N ILE D 690 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 693 " --> pdb=" O MET D 689 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Proline residue: D 698 - end of helix Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.542A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 3.807A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.810A pdb=" N SER D 753 " --> pdb=" O GLY D 749 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 792 through 810 removed outlier: 4.155A pdb=" N TYR D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 823 removed outlier: 4.081A pdb=" N GLN D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 846 Processing helix chain 'D' and resid 857 through 866 removed outlier: 3.956A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 885 Processing helix chain 'D' and resid 891 through 902 removed outlier: 3.553A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN D 902 " --> pdb=" O GLU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 919 Processing helix chain 'F' and resid 101 through 110 removed outlier: 3.690A pdb=" N LEU F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 132 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.782A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.989A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 23 removed outlier: 3.817A pdb=" N GLN S 23 " --> pdb=" O ILE S 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 20 through 23' Processing helix chain 'S' and resid 24 through 33 Processing helix chain 'S' and resid 51 through 65 removed outlier: 3.574A pdb=" N LYS S 56 " --> pdb=" O ALA S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 94 Processing helix chain 'S' and resid 96 through 111 removed outlier: 3.517A pdb=" N LEU S 105 " --> pdb=" O PHE S 101 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN S 108 " --> pdb=" O ILE S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 128 removed outlier: 3.670A pdb=" N LEU S 116 " --> pdb=" O ILE S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 139 removed outlier: 3.698A pdb=" N ARG S 136 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS S 137 " --> pdb=" O GLU S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 157 Processing sheet with id=AA1, first strand: chain 'C' and resid 536 through 541 removed outlier: 6.487A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 600 through 602 removed outlier: 3.604A pdb=" N VAL C 682 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 620 through 621 Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA5, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.702A pdb=" N ARG F 164 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET F 186 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 212 " --> pdb=" O MET F 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.529A pdb=" N ASN F 289 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AA8, first strand: chain 'S' and resid 13 through 17 removed outlier: 3.513A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE S 4 " --> pdb=" O VAL S 16 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2760 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: 9.00 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2315 1.32 - 1.44: 3338 1.44 - 1.56: 8053 1.56 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 13807 Sorted by residual: bond pdb=" C SER D 682 " pdb=" O SER D 682 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.19e-02 7.06e+03 1.21e+01 bond pdb=" CA SER D 682 " pdb=" CB SER D 682 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.59e-02 3.96e+03 1.20e+01 bond pdb=" CA SER F 135 " pdb=" CB SER F 135 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.58e-02 4.01e+03 8.95e+00 bond pdb=" N LEU F 136 " pdb=" CA LEU F 136 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.27e-02 6.20e+03 5.87e+00 bond pdb=" N SER D 682 " pdb=" CA SER D 682 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.52e+00 ... (remaining 13802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 18616 2.00 - 4.00: 215 4.00 - 6.00: 40 6.00 - 7.99: 5 7.99 - 9.99: 1 Bond angle restraints: 18877 Sorted by residual: angle pdb=" CA GLU F 134 " pdb=" C GLU F 134 " pdb=" N SER F 135 " ideal model delta sigma weight residual 118.43 111.87 6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" C LYS D 78 " pdb=" N VAL D 79 " pdb=" CA VAL D 79 " ideal model delta sigma weight residual 122.11 126.92 -4.81 1.12e+00 7.97e-01 1.85e+01 angle pdb=" C VAL D 432 " pdb=" CA VAL D 432 " pdb=" CB VAL D 432 " ideal model delta sigma weight residual 113.70 109.76 3.94 9.50e-01 1.11e+00 1.72e+01 angle pdb=" C ARG C 401 " pdb=" N PHE C 402 " pdb=" CA PHE C 402 " ideal model delta sigma weight residual 122.06 116.47 5.59 1.86e+00 2.89e-01 9.04e+00 angle pdb=" O GLU F 134 " pdb=" C GLU F 134 " pdb=" N SER F 135 " ideal model delta sigma weight residual 122.46 126.51 -4.05 1.38e+00 5.25e-01 8.61e+00 ... (remaining 18872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 7657 17.21 - 34.41: 508 34.41 - 51.62: 107 51.62 - 68.83: 19 68.83 - 86.03: 9 Dihedral angle restraints: 8300 sinusoidal: 2421 harmonic: 5879 Sorted by residual: dihedral pdb=" CA PHE D 532 " pdb=" C PHE D 532 " pdb=" N TYR D 533 " pdb=" CA TYR D 533 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER F 135 " pdb=" C SER F 135 " pdb=" N LEU F 136 " pdb=" CA LEU F 136 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA HIS C 143 " pdb=" C HIS C 143 " pdb=" N TRP C 144 " pdb=" CA TRP C 144 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1680 0.037 - 0.073: 542 0.073 - 0.110: 131 0.110 - 0.146: 21 0.146 - 0.183: 3 Chirality restraints: 2377 Sorted by residual: chirality pdb=" CA LEU D 181 " pdb=" N LEU D 181 " pdb=" C LEU D 181 " pdb=" CB LEU D 181 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA LEU F 136 " pdb=" N LEU F 136 " pdb=" C LEU F 136 " pdb=" CB LEU F 136 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA ASN D 662 " pdb=" N ASN D 662 " pdb=" C ASN D 662 " pdb=" CB ASN D 662 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 2374 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 134 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLU F 134 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU F 134 " 0.024 2.00e-02 2.50e+03 pdb=" N SER F 135 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 144 " -0.016 2.00e-02 2.50e+03 1.37e-02 4.67e+00 pdb=" CG TRP C 144 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 144 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 144 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 144 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 144 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 144 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 144 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 144 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 186 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO D 187 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " -0.029 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 352 2.72 - 3.26: 13958 3.26 - 3.81: 21533 3.81 - 4.35: 23122 4.35 - 4.90: 41782 Nonbonded interactions: 100747 Sorted by model distance: nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.173 3.040 nonbonded pdb=" OG SER S 24 " pdb=" O LEU S 110 " model vdw 2.203 3.040 nonbonded pdb=" O PHE D 383 " pdb=" NE2 GLN D 442 " model vdw 2.231 3.120 nonbonded pdb=" O ILE D 642 " pdb=" OH TYR D 681 " model vdw 2.252 3.040 nonbonded pdb=" O LEU D 776 " pdb=" OG1 THR D 780 " model vdw 2.254 3.040 ... (remaining 100742 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: 61.140 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: 0.030 Extract box with map and model: 34.190 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 41.080 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.150 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:5.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.003 0.055 13807 Z= 0.148 Angle : 0.570 9.992 18877 Z= 0.325 Chirality : 0.038 0.183 2377 Planarity : 0.004 0.051 2435 Dihedral : 13.023 86.035 4448 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1957 helix: 2.11 (0.14), residues: 1282 sheet: -2.80 (0.65), residues: 60 loop : -0.97 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 144 HIS 0.002 0.001 HIS C 345 PHE 0.021 0.001 PHE D 532 TYR 0.015 0.001 TYR C 366 ARG 0.004 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.17454 ( 936) hydrogen bonds : angle 4.80583 ( 2760) covalent geometry : bond 0.00288 (13807) covalent geometry : angle 0.56985 (18877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.701 Fit side-chains REVERT: C 189 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7965 (ttmm) REVERT: C 194 GLU cc_start: 0.7394 (mp0) cc_final: 0.6979 (mp0) REVERT: C 289 ARG cc_start: 0.7088 (ttp-170) cc_final: 0.6277 (ttp-110) REVERT: C 290 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8010 (tttm) REVERT: C 292 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7284 (mt-10) REVERT: C 294 VAL cc_start: 0.8383 (t) cc_final: 0.8054 (t) REVERT: C 330 GLN cc_start: 0.7805 (pp30) cc_final: 0.7522 (pp30) REVERT: C 386 ASN cc_start: 0.8223 (t0) cc_final: 0.8019 (t0) REVERT: C 641 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8086 (tt0) REVERT: C 743 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7883 (ttpp) REVERT: C 751 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7290 (ttmm) REVERT: D 51 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7645 (tmtt) REVERT: D 341 ASP cc_start: 0.7460 (p0) cc_final: 0.7259 (p0) REVERT: D 399 LEU cc_start: 0.8459 (mt) cc_final: 0.8241 (mt) REVERT: D 706 MET cc_start: 0.6666 (tpt) cc_final: 0.6358 (mmm) REVERT: D 757 ASP cc_start: 0.7148 (m-30) cc_final: 0.6939 (m-30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3668 time to fit residues: 169.2049 Evaluate side-chains 308 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 155 optimal weight: 0.0870 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 476 HIS C 505 GLN C 696 GLN C 737 GLN D 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111016 restraints weight = 22578.337| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.00 r_work: 0.3225 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13807 Z= 0.165 Angle : 0.537 11.161 18877 Z= 0.283 Chirality : 0.040 0.171 2377 Planarity : 0.004 0.054 2435 Dihedral : 3.598 18.536 2076 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.09 % Allowed : 10.37 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1957 helix: 2.15 (0.14), residues: 1319 sheet: -2.60 (0.66), residues: 60 loop : -0.94 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.026 0.002 PHE D 211 TYR 0.017 0.002 TYR D 533 ARG 0.003 0.000 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 936) hydrogen bonds : angle 3.85723 ( 2760) covalent geometry : bond 0.00380 (13807) covalent geometry : angle 0.53676 (18877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 1.486 Fit side-chains REVERT: C 131 LYS cc_start: 0.8240 (tppp) cc_final: 0.8034 (tppp) REVERT: C 190 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 194 GLU cc_start: 0.7947 (mp0) cc_final: 0.7468 (mp0) REVERT: C 286 GLU cc_start: 0.8099 (tp30) cc_final: 0.7761 (tp30) REVERT: C 289 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7644 (ttp-110) REVERT: C 292 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 330 GLN cc_start: 0.8229 (pp30) cc_final: 0.7877 (pp30) REVERT: C 372 ASP cc_start: 0.7750 (m-30) cc_final: 0.7538 (m-30) REVERT: C 485 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 641 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8198 (tt0) REVERT: C 708 LYS cc_start: 0.8280 (mttt) cc_final: 0.8055 (mtmm) REVERT: C 751 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7596 (ttmm) REVERT: C 754 ASP cc_start: 0.7965 (t70) cc_final: 0.7679 (t70) REVERT: D 104 ASP cc_start: 0.7884 (t70) cc_final: 0.7556 (t70) REVERT: D 112 THR cc_start: 0.8281 (p) cc_final: 0.8060 (t) REVERT: D 340 SER cc_start: 0.8795 (p) cc_final: 0.8532 (p) REVERT: D 341 ASP cc_start: 0.8188 (p0) cc_final: 0.7897 (p0) REVERT: D 757 ASP cc_start: 0.7720 (m-30) cc_final: 0.7479 (m-30) REVERT: D 765 THR cc_start: 0.8733 (t) cc_final: 0.8516 (p) outliers start: 24 outliers final: 12 residues processed: 314 average time/residue: 0.2570 time to fit residues: 117.2070 Evaluate side-chains 303 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 291 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 527 CYS Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain S residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111679 restraints weight = 22554.725| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.00 r_work: 0.3234 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.134 Angle : 0.508 10.747 18877 Z= 0.263 Chirality : 0.039 0.164 2377 Planarity : 0.004 0.051 2435 Dihedral : 3.519 18.152 2076 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.35 % Allowed : 12.63 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 1957 helix: 2.24 (0.14), residues: 1318 sheet: -2.58 (0.66), residues: 60 loop : -0.95 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.028 0.001 PHE C 251 TYR 0.015 0.001 TYR C 366 ARG 0.002 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 936) hydrogen bonds : angle 3.60318 ( 2760) covalent geometry : bond 0.00309 (13807) covalent geometry : angle 0.50778 (18877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 1.483 Fit side-chains REVERT: C 131 LYS cc_start: 0.8216 (tppp) cc_final: 0.7880 (tppp) REVERT: C 190 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 194 GLU cc_start: 0.7965 (mp0) cc_final: 0.7417 (mp0) REVERT: C 289 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7739 (ttp-170) REVERT: C 292 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 330 GLN cc_start: 0.8236 (pp30) cc_final: 0.7874 (pp30) REVERT: C 372 ASP cc_start: 0.7722 (m-30) cc_final: 0.7514 (m-30) REVERT: C 641 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8172 (tt0) REVERT: C 708 LYS cc_start: 0.8262 (mttt) cc_final: 0.8040 (mtmm) REVERT: C 751 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7571 (ttmm) REVERT: C 754 ASP cc_start: 0.7998 (t70) cc_final: 0.7671 (t0) REVERT: D 104 ASP cc_start: 0.7819 (t70) cc_final: 0.7497 (t70) REVERT: D 153 GLU cc_start: 0.7544 (mp0) cc_final: 0.7309 (mp0) REVERT: D 306 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8636 (p) REVERT: D 340 SER cc_start: 0.8778 (p) cc_final: 0.8572 (p) REVERT: D 341 ASP cc_start: 0.8173 (p0) cc_final: 0.7889 (p0) REVERT: D 757 ASP cc_start: 0.7699 (m-30) cc_final: 0.7412 (m-30) REVERT: S 102 GLU cc_start: 0.7705 (tp30) cc_final: 0.7497 (tp30) outliers start: 27 outliers final: 15 residues processed: 301 average time/residue: 0.2639 time to fit residues: 114.7861 Evaluate side-chains 299 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 283 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 112 optimal weight: 0.0270 chunk 52 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112264 restraints weight = 22521.039| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.00 r_work: 0.3246 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.117 Angle : 0.493 11.078 18877 Z= 0.254 Chirality : 0.038 0.167 2377 Planarity : 0.004 0.049 2435 Dihedral : 3.421 17.845 2076 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.35 % Allowed : 14.63 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1957 helix: 2.38 (0.14), residues: 1317 sheet: -2.47 (0.67), residues: 60 loop : -0.90 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 144 HIS 0.002 0.001 HIS C 727 PHE 0.029 0.001 PHE D 211 TYR 0.023 0.001 TYR C 42 ARG 0.003 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 936) hydrogen bonds : angle 3.47663 ( 2760) covalent geometry : bond 0.00263 (13807) covalent geometry : angle 0.49345 (18877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 1.433 Fit side-chains REVERT: C 41 ARG cc_start: 0.8372 (tpt90) cc_final: 0.8102 (tpt170) REVERT: C 131 LYS cc_start: 0.8198 (tppp) cc_final: 0.7907 (tppp) REVERT: C 190 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8115 (tm-30) REVERT: C 194 GLU cc_start: 0.7942 (mp0) cc_final: 0.7436 (mp0) REVERT: C 289 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: C 292 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 330 GLN cc_start: 0.8209 (pp30) cc_final: 0.7823 (pp30) REVERT: C 372 ASP cc_start: 0.7692 (m-30) cc_final: 0.7484 (m-30) REVERT: C 641 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8209 (tp40) REVERT: C 648 LEU cc_start: 0.8120 (mp) cc_final: 0.7766 (tt) REVERT: C 708 LYS cc_start: 0.8271 (mttt) cc_final: 0.8046 (mtmm) REVERT: C 751 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7558 (ttmm) REVERT: C 754 ASP cc_start: 0.7985 (t70) cc_final: 0.7656 (t0) REVERT: D 104 ASP cc_start: 0.7803 (t70) cc_final: 0.7502 (m-30) REVERT: D 306 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 341 ASP cc_start: 0.8201 (p0) cc_final: 0.7894 (p0) REVERT: D 757 ASP cc_start: 0.7686 (m-30) cc_final: 0.7405 (m-30) outliers start: 27 outliers final: 16 residues processed: 293 average time/residue: 0.2656 time to fit residues: 111.3858 Evaluate side-chains 298 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 0.0000 chunk 166 optimal weight: 0.1980 chunk 158 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 168 optimal weight: 30.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 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 = 0.3849 r_free = 0.3849 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113110 restraints weight = 22592.448| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.00 r_work: 0.3250 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13807 Z= 0.109 Angle : 0.492 11.281 18877 Z= 0.250 Chirality : 0.037 0.167 2377 Planarity : 0.004 0.047 2435 Dihedral : 3.336 17.298 2076 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.18 % Allowed : 15.94 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1957 helix: 2.46 (0.14), residues: 1321 sheet: -2.40 (0.67), residues: 60 loop : -0.83 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 144 HIS 0.002 0.001 HIS D 707 PHE 0.018 0.001 PHE C 251 TYR 0.019 0.001 TYR C 42 ARG 0.003 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 936) hydrogen bonds : angle 3.38046 ( 2760) covalent geometry : bond 0.00243 (13807) covalent geometry : angle 0.49195 (18877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 1.631 Fit side-chains REVERT: C 37 MET cc_start: 0.7634 (tpt) cc_final: 0.7403 (tpt) REVERT: C 131 LYS cc_start: 0.8168 (tppp) cc_final: 0.7893 (tppp) REVERT: C 190 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8129 (tm-30) REVERT: C 194 GLU cc_start: 0.7935 (mp0) cc_final: 0.7411 (mp0) REVERT: C 289 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: C 292 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7794 (mt-10) REVERT: C 330 GLN cc_start: 0.8201 (pp30) cc_final: 0.7797 (pp30) REVERT: C 372 ASP cc_start: 0.7669 (m-30) cc_final: 0.7462 (m-30) REVERT: C 478 ASN cc_start: 0.8405 (p0) cc_final: 0.8133 (p0) REVERT: C 485 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7155 (mm-30) REVERT: C 641 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7952 (tp-100) REVERT: C 648 LEU cc_start: 0.8125 (mp) cc_final: 0.7786 (tt) REVERT: C 751 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7547 (ttmm) REVERT: C 754 ASP cc_start: 0.8015 (t70) cc_final: 0.7674 (t0) REVERT: D 104 ASP cc_start: 0.7757 (t70) cc_final: 0.7509 (m-30) REVERT: D 211 PHE cc_start: 0.8110 (t80) cc_final: 0.7748 (t80) REVERT: D 257 ILE cc_start: 0.8835 (mm) cc_final: 0.8581 (mt) REVERT: D 306 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 341 ASP cc_start: 0.8182 (p0) cc_final: 0.7913 (p0) REVERT: D 366 GLU cc_start: 0.7625 (mp0) cc_final: 0.7300 (mp0) REVERT: D 757 ASP cc_start: 0.7616 (m-30) cc_final: 0.7330 (m-30) outliers start: 25 outliers final: 15 residues processed: 309 average time/residue: 0.2703 time to fit residues: 118.4637 Evaluate side-chains 301 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Chi-restraints excluded: chain S residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 53 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 168 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 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 = 0.3828 r_free = 0.3828 target = 0.142228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111565 restraints weight = 22866.642| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.131 Angle : 0.510 11.318 18877 Z= 0.260 Chirality : 0.038 0.153 2377 Planarity : 0.004 0.048 2435 Dihedral : 3.371 17.585 2076 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.35 % Allowed : 16.64 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 1957 helix: 2.40 (0.14), residues: 1325 sheet: -2.32 (0.65), residues: 62 loop : -0.79 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.019 0.001 PHE C 402 TYR 0.022 0.001 TYR C 42 ARG 0.004 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 936) hydrogen bonds : angle 3.40914 ( 2760) covalent geometry : bond 0.00305 (13807) covalent geometry : angle 0.51001 (18877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 292 time to evaluate : 1.657 Fit side-chains REVERT: C 37 MET cc_start: 0.7637 (tpt) cc_final: 0.7436 (tpt) REVERT: C 41 ARG cc_start: 0.8291 (tpt90) cc_final: 0.8037 (tpt90) REVERT: C 131 LYS cc_start: 0.8180 (tppp) cc_final: 0.7887 (tppp) REVERT: C 286 GLU cc_start: 0.8156 (tp30) cc_final: 0.7661 (tp30) REVERT: C 289 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7387 (ttp-170) REVERT: C 292 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7831 (mt-10) REVERT: C 330 GLN cc_start: 0.8208 (pp30) cc_final: 0.7808 (pp30) REVERT: C 372 ASP cc_start: 0.7720 (m-30) cc_final: 0.7509 (m-30) REVERT: C 485 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 641 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8225 (tp40) REVERT: C 648 LEU cc_start: 0.8171 (mp) cc_final: 0.7857 (tt) REVERT: C 708 LYS cc_start: 0.8237 (mttt) cc_final: 0.8014 (mtmm) REVERT: C 751 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7565 (ttmm) REVERT: C 754 ASP cc_start: 0.8004 (t70) cc_final: 0.7677 (t0) REVERT: D 104 ASP cc_start: 0.7839 (t70) cc_final: 0.7540 (m-30) REVERT: D 257 ILE cc_start: 0.8859 (mm) cc_final: 0.8623 (mt) REVERT: D 306 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (p) REVERT: D 341 ASP cc_start: 0.8152 (p0) cc_final: 0.7867 (p0) REVERT: D 366 GLU cc_start: 0.7628 (mp0) cc_final: 0.7318 (mp0) REVERT: D 757 ASP cc_start: 0.7573 (m-30) cc_final: 0.7284 (m-30) outliers start: 27 outliers final: 21 residues processed: 305 average time/residue: 0.2708 time to fit residues: 118.8728 Evaluate side-chains 310 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 123 optimal weight: 1.9990 chunk 174 optimal weight: 50.0000 chunk 52 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 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 = 0.3825 r_free = 0.3825 target = 0.141948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111455 restraints weight = 22623.085| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.99 r_work: 0.3234 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.128 Angle : 0.503 11.251 18877 Z= 0.257 Chirality : 0.038 0.143 2377 Planarity : 0.004 0.048 2435 Dihedral : 3.376 17.634 2076 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.53 % Allowed : 16.99 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1957 helix: 2.35 (0.14), residues: 1338 sheet: -2.28 (0.65), residues: 62 loop : -0.90 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.019 0.001 PHE C 402 TYR 0.021 0.001 TYR C 42 ARG 0.004 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 936) hydrogen bonds : angle 3.39133 ( 2760) covalent geometry : bond 0.00297 (13807) covalent geometry : angle 0.50323 (18877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: C 18 ASP cc_start: 0.7923 (p0) cc_final: 0.7713 (p0) REVERT: C 41 ARG cc_start: 0.8261 (tpt90) cc_final: 0.8043 (tpt170) REVERT: C 131 LYS cc_start: 0.8173 (tppp) cc_final: 0.7884 (tppp) REVERT: C 194 GLU cc_start: 0.7945 (mp0) cc_final: 0.7497 (mp0) REVERT: C 292 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7836 (mt-10) REVERT: C 330 GLN cc_start: 0.8210 (pp30) cc_final: 0.7974 (pp30) REVERT: C 372 ASP cc_start: 0.7722 (m-30) cc_final: 0.7511 (m-30) REVERT: C 485 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7132 (mm-30) REVERT: C 641 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8235 (tp40) REVERT: C 648 LEU cc_start: 0.8220 (mp) cc_final: 0.7872 (tt) REVERT: C 708 LYS cc_start: 0.8213 (mttt) cc_final: 0.7986 (mtmm) REVERT: C 751 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7543 (ttmm) REVERT: C 754 ASP cc_start: 0.8002 (t70) cc_final: 0.7673 (t0) REVERT: D 104 ASP cc_start: 0.7836 (t70) cc_final: 0.7548 (m-30) REVERT: D 257 ILE cc_start: 0.8853 (mm) cc_final: 0.8633 (mt) REVERT: D 306 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (p) REVERT: D 341 ASP cc_start: 0.8150 (p0) cc_final: 0.7854 (p0) REVERT: D 366 GLU cc_start: 0.7613 (mp0) cc_final: 0.7312 (mp0) REVERT: D 757 ASP cc_start: 0.7608 (m-30) cc_final: 0.7273 (m-30) REVERT: D 760 GLN cc_start: 0.8478 (mt0) cc_final: 0.8240 (mt0) REVERT: S 65 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5880 (t-90) outliers start: 29 outliers final: 22 residues processed: 303 average time/residue: 0.2647 time to fit residues: 115.0310 Evaluate side-chains 313 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 65 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 129 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN S 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110036 restraints weight = 22516.495| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.99 r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13807 Z= 0.157 Angle : 0.532 11.456 18877 Z= 0.272 Chirality : 0.040 0.174 2377 Planarity : 0.004 0.049 2435 Dihedral : 3.500 18.774 2076 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.87 % Allowed : 16.90 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1957 helix: 2.24 (0.14), residues: 1332 sheet: -2.41 (0.63), residues: 62 loop : -0.92 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.022 0.001 PHE C 402 TYR 0.021 0.001 TYR C 42 ARG 0.005 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 936) hydrogen bonds : angle 3.50160 ( 2760) covalent geometry : bond 0.00369 (13807) covalent geometry : angle 0.53211 (18877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 1.417 Fit side-chains REVERT: C 41 ARG cc_start: 0.8220 (tpt90) cc_final: 0.7959 (tpt170) REVERT: C 131 LYS cc_start: 0.8170 (tppp) cc_final: 0.7824 (tppp) REVERT: C 194 GLU cc_start: 0.7958 (mp0) cc_final: 0.7500 (mp0) REVERT: C 289 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7598 (ttp-170) REVERT: C 292 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 641 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8239 (tp40) REVERT: C 648 LEU cc_start: 0.8246 (mp) cc_final: 0.7919 (tt) REVERT: C 708 LYS cc_start: 0.8228 (mttt) cc_final: 0.7995 (mtmm) REVERT: C 751 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7556 (ttmm) REVERT: C 754 ASP cc_start: 0.7999 (t70) cc_final: 0.7672 (t0) REVERT: D 104 ASP cc_start: 0.7911 (t70) cc_final: 0.7604 (m-30) REVERT: D 257 ILE cc_start: 0.8871 (mm) cc_final: 0.8668 (mt) REVERT: D 306 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8612 (p) REVERT: D 341 ASP cc_start: 0.8136 (p0) cc_final: 0.7830 (p0) REVERT: D 366 GLU cc_start: 0.7656 (mp0) cc_final: 0.7364 (mp0) REVERT: D 757 ASP cc_start: 0.7628 (m-30) cc_final: 0.7267 (m-30) REVERT: D 760 GLN cc_start: 0.8468 (mt0) cc_final: 0.8230 (mt0) outliers start: 33 outliers final: 26 residues processed: 300 average time/residue: 0.2621 time to fit residues: 113.1589 Evaluate side-chains 307 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 65 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 104 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 194 optimal weight: 0.2980 chunk 162 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN C 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112274 restraints weight = 22464.326| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.98 r_work: 0.3252 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13807 Z= 0.109 Angle : 0.502 11.452 18877 Z= 0.255 Chirality : 0.038 0.139 2377 Planarity : 0.004 0.047 2435 Dihedral : 3.355 17.256 2076 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.44 % Allowed : 17.86 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1957 helix: 2.41 (0.14), residues: 1335 sheet: -2.29 (0.65), residues: 62 loop : -0.92 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 144 HIS 0.011 0.001 HIS S 65 PHE 0.016 0.001 PHE C 402 TYR 0.022 0.001 TYR C 42 ARG 0.004 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 936) hydrogen bonds : angle 3.35143 ( 2760) covalent geometry : bond 0.00239 (13807) covalent geometry : angle 0.50236 (18877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: C 41 ARG cc_start: 0.8175 (tpt90) cc_final: 0.7965 (tpt170) REVERT: C 194 GLU cc_start: 0.7944 (mp0) cc_final: 0.7497 (mp0) REVERT: C 284 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7232 (tp40) REVERT: C 478 ASN cc_start: 0.8426 (p0) cc_final: 0.8143 (p0) REVERT: C 641 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8228 (tp40) REVERT: C 648 LEU cc_start: 0.8188 (mp) cc_final: 0.7900 (tt) REVERT: C 751 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7561 (ttmm) REVERT: C 754 ASP cc_start: 0.8023 (t70) cc_final: 0.7693 (t0) REVERT: D 104 ASP cc_start: 0.7808 (t70) cc_final: 0.7525 (m-30) REVERT: D 153 GLU cc_start: 0.7433 (mp0) cc_final: 0.7229 (mp0) REVERT: D 257 ILE cc_start: 0.8832 (mm) cc_final: 0.8609 (mt) REVERT: D 306 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 341 ASP cc_start: 0.8116 (p0) cc_final: 0.7808 (p0) REVERT: D 366 GLU cc_start: 0.7589 (mp0) cc_final: 0.7296 (mp0) REVERT: D 635 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8427 (mt) REVERT: D 706 MET cc_start: 0.7974 (tpt) cc_final: 0.7666 (mmm) REVERT: D 757 ASP cc_start: 0.7551 (m-30) cc_final: 0.7196 (m-30) REVERT: D 760 GLN cc_start: 0.8387 (mt0) cc_final: 0.8141 (mt0) REVERT: S 65 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.6191 (t-90) outliers start: 28 outliers final: 19 residues processed: 298 average time/residue: 0.2675 time to fit residues: 113.1900 Evaluate side-chains 307 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 65 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 49 optimal weight: 0.0030 chunk 68 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 72 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN C 374 HIS C 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113178 restraints weight = 22516.340| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.99 r_work: 0.3263 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13807 Z= 0.103 Angle : 0.505 11.654 18877 Z= 0.254 Chirality : 0.037 0.135 2377 Planarity : 0.004 0.047 2435 Dihedral : 3.305 20.894 2076 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.09 % Allowed : 18.21 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.20), residues: 1957 helix: 2.51 (0.14), residues: 1326 sheet: -2.22 (0.66), residues: 62 loop : -0.91 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 144 HIS 0.002 0.001 HIS C 299 PHE 0.015 0.001 PHE C 402 TYR 0.022 0.001 TYR C 42 ARG 0.004 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 936) hydrogen bonds : angle 3.30514 ( 2760) covalent geometry : bond 0.00225 (13807) covalent geometry : angle 0.50454 (18877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 290 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: C 41 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7940 (tpt170) REVERT: C 194 GLU cc_start: 0.7935 (mp0) cc_final: 0.7470 (mp0) REVERT: C 284 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: C 478 ASN cc_start: 0.8362 (p0) cc_final: 0.8098 (p0) REVERT: C 485 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7056 (mm-30) REVERT: C 641 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8240 (tp40) REVERT: C 648 LEU cc_start: 0.8199 (mp) cc_final: 0.7929 (tt) REVERT: C 751 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7547 (ttmm) REVERT: C 754 ASP cc_start: 0.8009 (t70) cc_final: 0.7668 (t0) REVERT: D 153 GLU cc_start: 0.7444 (mp0) cc_final: 0.7222 (mp0) REVERT: D 257 ILE cc_start: 0.8821 (mm) cc_final: 0.8593 (mt) REVERT: D 341 ASP cc_start: 0.8118 (p0) cc_final: 0.7814 (p0) REVERT: D 366 GLU cc_start: 0.7608 (mp0) cc_final: 0.7311 (mp0) REVERT: D 635 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8415 (mt) REVERT: D 706 MET cc_start: 0.7968 (tpt) cc_final: 0.7663 (mmm) REVERT: D 757 ASP cc_start: 0.7549 (m-30) cc_final: 0.7184 (m-30) REVERT: D 760 GLN cc_start: 0.8397 (mt0) cc_final: 0.8146 (mt0) REVERT: S 65 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.6012 (t-90) outliers start: 24 outliers final: 18 residues processed: 299 average time/residue: 0.2730 time to fit residues: 116.4532 Evaluate side-chains 303 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 820 GLN Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 65 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 131 optimal weight: 0.0370 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112022 restraints weight = 22784.685| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.00 r_work: 0.3246 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13807 Z= 0.120 Angle : 0.519 11.444 18877 Z= 0.261 Chirality : 0.038 0.172 2377 Planarity : 0.004 0.047 2435 Dihedral : 3.292 16.967 2076 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.92 % Allowed : 19.34 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1957 helix: 2.47 (0.14), residues: 1327 sheet: -2.24 (0.65), residues: 62 loop : -0.90 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 144 HIS 0.002 0.001 HIS C 727 PHE 0.018 0.001 PHE C 402 TYR 0.021 0.001 TYR C 42 ARG 0.004 0.000 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 936) hydrogen bonds : angle 3.33545 ( 2760) covalent geometry : bond 0.00276 (13807) covalent geometry : angle 0.51861 (18877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9790.70 seconds wall clock time: 168 minutes 47.62 seconds (10127.62 seconds total)