Starting phenix.real_space_refine on Thu May 15 19:48:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdj_16575/05_2025/8cdj_16575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdj_16575/05_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_16575/05_2025/8cdj_16575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdj_16575/05_2025/8cdj_16575.map" model { file = "/net/cci-nas-00/data/ceres_data/8cdj_16575/05_2025/8cdj_16575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdj_16575/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.81, per 1000 atoms: 0.57 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 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: 1.39 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: 4.58 Time building geometry restraints manager: 3.62 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: 4.380 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 30.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- 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 : 1.609 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: 0.2709 time to fit residues: 123.1698 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 : 1.351 ------------------------------------------------------------------------------- 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 = 74)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111027 restraints weight = 22578.334| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.00 r_work: 0.3221 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- 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 : 1.507 Fit side-chains REVERT: C 131 LYS cc_start: 0.8239 (tppp) cc_final: 0.8032 (tppp) REVERT: C 190 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 194 GLU cc_start: 0.7938 (mp0) cc_final: 0.7461 (mp0) REVERT: C 286 GLU cc_start: 0.8099 (tp30) cc_final: 0.7761 (tp30) REVERT: C 289 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7637 (ttp-110) REVERT: C 292 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 330 GLN cc_start: 0.8228 (pp30) cc_final: 0.7877 (pp30) REVERT: C 372 ASP cc_start: 0.7750 (m-30) cc_final: 0.7535 (m-30) REVERT: C 485 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 641 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8200 (tt0) REVERT: C 708 LYS cc_start: 0.8283 (mttt) cc_final: 0.8059 (mtmm) REVERT: C 751 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7603 (ttmm) REVERT: C 754 ASP cc_start: 0.7961 (t70) cc_final: 0.7673 (t70) REVERT: D 104 ASP cc_start: 0.7878 (t70) cc_final: 0.7551 (t70) REVERT: D 112 THR cc_start: 0.8282 (p) cc_final: 0.8059 (t) REVERT: D 340 SER cc_start: 0.8790 (p) cc_final: 0.8526 (p) REVERT: D 341 ASP cc_start: 0.8186 (p0) cc_final: 0.7895 (p0) REVERT: D 757 ASP cc_start: 0.7723 (m-30) cc_final: 0.7483 (m-30) REVERT: D 765 THR cc_start: 0.8734 (t) cc_final: 0.8517 (p) outliers start: 24 outliers final: 12 residues processed: 314 average time/residue: 0.2640 time to fit residues: 120.9597 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 : 1.466 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 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 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 = 0.142446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111502 restraints weight = 22568.965| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.00 r_work: 0.3234 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13807 Z= 0.135 Angle : 0.506 10.844 18877 Z= 0.262 Chirality : 0.039 0.161 2377 Planarity : 0.004 0.051 2435 Dihedral : 3.518 18.227 2076 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.44 % Allowed : 12.46 % Favored : 85.10 % 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 0.026 0.001 TRP C 144 HIS 0.002 0.001 HIS C 727 PHE 0.029 0.001 PHE C 251 TYR 0.015 0.001 TYR C 366 ARG 0.003 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 936) hydrogen bonds : angle 3.60152 ( 2760) covalent geometry : bond 0.00307 (13807) covalent geometry : angle 0.50601 (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 315 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 1.500 Fit side-chains REVERT: C 131 LYS cc_start: 0.8226 (tppp) cc_final: 0.7889 (tppp) REVERT: C 190 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 194 GLU cc_start: 0.7963 (mp0) cc_final: 0.7436 (mp0) REVERT: C 289 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7744 (ttp-170) REVERT: C 292 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7826 (mt-10) REVERT: C 330 GLN cc_start: 0.8233 (pp30) cc_final: 0.7870 (pp30) REVERT: C 372 ASP cc_start: 0.7719 (m-30) cc_final: 0.7512 (m-30) REVERT: C 641 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8173 (tt0) REVERT: C 708 LYS cc_start: 0.8254 (mttt) cc_final: 0.8033 (mtmm) REVERT: C 751 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7565 (ttmm) REVERT: C 754 ASP cc_start: 0.7989 (t70) cc_final: 0.7662 (t0) REVERT: D 104 ASP cc_start: 0.7816 (t70) cc_final: 0.7492 (t70) REVERT: D 153 GLU cc_start: 0.7536 (mp0) cc_final: 0.7301 (mp0) REVERT: D 306 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8639 (p) REVERT: D 340 SER cc_start: 0.8775 (p) cc_final: 0.8567 (p) REVERT: D 341 ASP cc_start: 0.8198 (p0) cc_final: 0.7906 (p0) REVERT: D 757 ASP cc_start: 0.7701 (m-30) cc_final: 0.7413 (m-30) REVERT: S 102 GLU cc_start: 0.7709 (tp30) cc_final: 0.7500 (tp30) outliers start: 28 outliers final: 17 residues processed: 302 average time/residue: 0.2746 time to fit residues: 119.7994 Evaluate side-chains 303 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 399 LEU 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.142681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112044 restraints weight = 22532.066| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.01 r_work: 0.3241 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1710 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= 0.122 Angle : 0.495 10.773 18877 Z= 0.255 Chirality : 0.038 0.167 2377 Planarity : 0.004 0.049 2435 Dihedral : 3.431 17.759 2076 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.44 % Allowed : 14.46 % Favored : 83.10 % 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: 1.94 (0.19), residues: 1957 helix: 2.38 (0.14), residues: 1315 sheet: -2.49 (0.67), residues: 60 loop : -0.91 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 144 HIS 0.002 0.001 HIS C 727 PHE 0.028 0.001 PHE D 211 TYR 0.024 0.001 TYR C 42 ARG 0.003 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 936) hydrogen bonds : angle 3.47433 ( 2760) covalent geometry : bond 0.00276 (13807) covalent geometry : angle 0.49497 (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 318 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 1.373 Fit side-chains REVERT: C 41 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8144 (tpt90) REVERT: C 131 LYS cc_start: 0.8191 (tppp) cc_final: 0.7894 (tppp) REVERT: C 190 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 194 GLU cc_start: 0.7934 (mp0) cc_final: 0.7438 (mp0) REVERT: C 289 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7886 (ttp-170) REVERT: C 292 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 372 ASP cc_start: 0.7696 (m-30) cc_final: 0.7486 (m-30) REVERT: C 641 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8214 (tp40) REVERT: C 648 LEU cc_start: 0.8129 (mp) cc_final: 0.7791 (tt) REVERT: C 708 LYS cc_start: 0.8277 (mttt) cc_final: 0.8037 (mtmm) REVERT: C 751 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7569 (ttmm) REVERT: C 754 ASP cc_start: 0.7999 (t70) cc_final: 0.7665 (t0) REVERT: D 104 ASP cc_start: 0.7807 (t70) cc_final: 0.7508 (m-30) REVERT: D 257 ILE cc_start: 0.8855 (mm) cc_final: 0.8613 (mt) REVERT: D 306 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 341 ASP cc_start: 0.8201 (p0) cc_final: 0.7901 (p0) REVERT: D 534 LYS cc_start: 0.7731 (mttp) cc_final: 0.7504 (mttp) REVERT: D 757 ASP cc_start: 0.7699 (m-30) cc_final: 0.7415 (m-30) outliers start: 28 outliers final: 15 residues processed: 303 average time/residue: 0.2466 time to fit residues: 107.6963 Evaluate side-chains 300 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 chunk 150 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 168 optimal weight: 30.0000 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.141571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110953 restraints weight = 22564.597| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.00 r_work: 0.3224 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13807 Z= 0.138 Angle : 0.510 11.006 18877 Z= 0.263 Chirality : 0.039 0.165 2377 Planarity : 0.004 0.049 2435 Dihedral : 3.439 18.138 2076 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.35 % Allowed : 15.51 % Favored : 82.14 % 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: 1.92 (0.19), residues: 1957 helix: 2.33 (0.14), residues: 1318 sheet: -2.50 (0.66), residues: 60 loop : -0.84 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 144 HIS 0.003 0.001 HIS C 727 PHE 0.029 0.001 PHE D 211 TYR 0.020 0.001 TYR C 42 ARG 0.004 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 936) hydrogen bonds : angle 3.46784 ( 2760) covalent geometry : bond 0.00322 (13807) covalent geometry : angle 0.51047 (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 318 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 1.574 Fit side-chains REVERT: C 37 MET cc_start: 0.7660 (tpt) cc_final: 0.7448 (tpt) REVERT: C 131 LYS cc_start: 0.8184 (tppp) cc_final: 0.7824 (tppp) REVERT: C 190 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8127 (tm-30) REVERT: C 194 GLU cc_start: 0.7953 (mp0) cc_final: 0.7474 (mp0) REVERT: C 286 GLU cc_start: 0.8160 (tp30) cc_final: 0.7702 (tp30) REVERT: C 289 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7328 (ttp-170) REVERT: C 292 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 485 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 641 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8226 (tp40) REVERT: C 648 LEU cc_start: 0.8186 (mp) cc_final: 0.7842 (tt) REVERT: C 708 LYS cc_start: 0.8268 (mttt) cc_final: 0.8044 (mtmm) REVERT: C 751 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7580 (ttmm) REVERT: C 754 ASP cc_start: 0.8018 (t70) cc_final: 0.7693 (t0) REVERT: D 104 ASP cc_start: 0.7833 (t70) cc_final: 0.7552 (m-30) REVERT: D 257 ILE cc_start: 0.8864 (mm) cc_final: 0.8638 (mt) REVERT: D 306 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8614 (p) REVERT: D 341 ASP cc_start: 0.8142 (p0) cc_final: 0.7855 (p0) REVERT: D 366 GLU cc_start: 0.7607 (mp0) cc_final: 0.7300 (mp0) REVERT: D 757 ASP cc_start: 0.7676 (m-30) cc_final: 0.7389 (m-30) outliers start: 27 outliers final: 19 residues processed: 304 average time/residue: 0.2460 time to fit residues: 108.0892 Evaluate side-chains 304 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 537 ILE 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 138 LEU 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: 9.9990 chunk 12 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 168 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109785 restraints weight = 22859.131| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.01 r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2017 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= 0.162 Angle : 0.532 11.019 18877 Z= 0.274 Chirality : 0.040 0.177 2377 Planarity : 0.004 0.050 2435 Dihedral : 3.543 19.124 2076 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.79 % Allowed : 15.94 % Favored : 81.27 % 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: 1.80 (0.19), residues: 1957 helix: 2.22 (0.14), residues: 1321 sheet: -2.50 (0.63), residues: 62 loop : -0.83 (0.24), residues: 574 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 0.031 0.002 PHE D 211 TYR 0.021 0.001 TYR C 42 ARG 0.005 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 936) hydrogen bonds : angle 3.53431 ( 2760) covalent geometry : bond 0.00383 (13807) covalent geometry : angle 0.53207 (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 327 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: C 131 LYS cc_start: 0.8175 (tppp) cc_final: 0.7825 (tppp) REVERT: C 194 GLU cc_start: 0.7969 (mp0) cc_final: 0.7512 (mp0) REVERT: C 292 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 641 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8227 (tp40) REVERT: C 648 LEU cc_start: 0.8272 (mp) cc_final: 0.7908 (tt) REVERT: C 695 GLU cc_start: 0.7623 (tt0) cc_final: 0.7394 (tt0) REVERT: C 751 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7546 (ttmm) REVERT: C 754 ASP cc_start: 0.8023 (t70) cc_final: 0.7698 (t0) REVERT: D 104 ASP cc_start: 0.7894 (t70) cc_final: 0.7572 (m-30) REVERT: D 257 ILE cc_start: 0.8864 (mm) cc_final: 0.8664 (mt) REVERT: D 341 ASP cc_start: 0.8150 (p0) cc_final: 0.7867 (p0) REVERT: D 366 GLU cc_start: 0.7638 (mp0) cc_final: 0.7341 (mp0) REVERT: D 757 ASP cc_start: 0.7612 (m-30) cc_final: 0.7257 (m-30) outliers start: 32 outliers final: 27 residues processed: 312 average time/residue: 0.2499 time to fit residues: 112.8277 Evaluate side-chains 318 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 537 ILE 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 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 600 LEU Chi-restraints excluded: chain D residue 683 ASP 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: 0.9980 chunk 174 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.140652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110036 restraints weight = 22609.034| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.99 r_work: 0.3207 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13807 Z= 0.150 Angle : 0.526 10.935 18877 Z= 0.271 Chirality : 0.039 0.170 2377 Planarity : 0.004 0.050 2435 Dihedral : 3.543 18.681 2076 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.31 % Allowed : 16.64 % Favored : 80.05 % 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: 1.73 (0.19), residues: 1957 helix: 2.17 (0.14), residues: 1334 sheet: -2.44 (0.63), residues: 62 loop : -0.97 (0.24), residues: 561 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 0.033 0.001 PHE D 211 TYR 0.021 0.001 TYR C 42 ARG 0.004 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 936) hydrogen bonds : angle 3.50917 ( 2760) covalent geometry : bond 0.00353 (13807) covalent geometry : angle 0.52551 (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: 38 poor density : 279 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: C 131 LYS cc_start: 0.8183 (tppp) cc_final: 0.7826 (tppp) REVERT: C 190 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 194 GLU cc_start: 0.7948 (mp0) cc_final: 0.7594 (mp0) REVERT: C 292 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 641 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8242 (tp40) REVERT: C 648 LEU cc_start: 0.8241 (mp) cc_final: 0.7914 (tt) REVERT: C 751 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7539 (ttmm) REVERT: C 754 ASP cc_start: 0.8032 (t70) cc_final: 0.7703 (t0) REVERT: D 104 ASP cc_start: 0.7886 (t70) cc_final: 0.7570 (m-30) REVERT: D 257 ILE cc_start: 0.8859 (mm) cc_final: 0.8657 (mt) REVERT: D 341 ASP cc_start: 0.8144 (p0) cc_final: 0.7832 (p0) REVERT: D 366 GLU cc_start: 0.7650 (mp0) cc_final: 0.7358 (mp0) REVERT: D 534 LYS cc_start: 0.7975 (mttp) cc_final: 0.7694 (mttp) REVERT: D 757 ASP cc_start: 0.7629 (m-30) cc_final: 0.7324 (m-30) REVERT: S 65 HIS cc_start: 0.6277 (OUTLIER) cc_final: 0.5849 (t-90) outliers start: 38 outliers final: 26 residues processed: 299 average time/residue: 0.2612 time to fit residues: 112.3050 Evaluate side-chains 304 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 537 ILE 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 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 477 VAL Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 683 ASP 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: 0.9980 chunk 151 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 159 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 S 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109319 restraints weight = 22511.143| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.00 r_work: 0.3197 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13807 Z= 0.164 Angle : 0.544 11.055 18877 Z= 0.280 Chirality : 0.040 0.191 2377 Planarity : 0.004 0.051 2435 Dihedral : 3.592 19.264 2076 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.22 % Allowed : 17.42 % Favored : 79.36 % 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: 1.67 (0.19), residues: 1957 helix: 2.14 (0.14), residues: 1331 sheet: -2.50 (0.63), residues: 62 loop : -1.02 (0.24), residues: 564 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 0.034 0.002 PHE D 211 TYR 0.019 0.001 TYR C 42 ARG 0.010 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 936) hydrogen bonds : angle 3.54929 ( 2760) covalent geometry : bond 0.00388 (13807) covalent geometry : angle 0.54371 (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 321 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.348 Fit side-chains REVERT: C 131 LYS cc_start: 0.8185 (tppp) cc_final: 0.7854 (tppp) REVERT: C 194 GLU cc_start: 0.7936 (mp0) cc_final: 0.7461 (mp0) REVERT: C 284 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7230 (tp40) REVERT: C 289 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7446 (ttp-170) REVERT: C 292 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 641 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8230 (tp40) REVERT: C 648 LEU cc_start: 0.8274 (mp) cc_final: 0.7972 (tt) REVERT: C 695 GLU cc_start: 0.7612 (tt0) cc_final: 0.7387 (tt0) REVERT: C 751 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7546 (ttmm) REVERT: C 754 ASP cc_start: 0.8026 (t70) cc_final: 0.7697 (t0) REVERT: D 341 ASP cc_start: 0.8128 (p0) cc_final: 0.7822 (p0) REVERT: D 366 GLU cc_start: 0.7670 (mp0) cc_final: 0.7382 (mp0) REVERT: D 757 ASP cc_start: 0.7633 (m-30) cc_final: 0.7317 (m-30) outliers start: 37 outliers final: 27 residues processed: 303 average time/residue: 0.2801 time to fit residues: 123.1987 Evaluate side-chains 312 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 LEU 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 537 ILE 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 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 600 LEU Chi-restraints excluded: chain D residue 683 ASP 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: 5.9990 chunk 7 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 40.0000 chunk 194 optimal weight: 0.5980 chunk 162 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 180 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110658 restraints weight = 22412.714| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.99 r_work: 0.3212 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2300 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 : 0.531 11.385 18877 Z= 0.272 Chirality : 0.039 0.152 2377 Planarity : 0.004 0.055 2435 Dihedral : 3.513 18.427 2076 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.44 % Allowed : 18.82 % 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: 1.77 (0.19), residues: 1957 helix: 2.22 (0.14), residues: 1333 sheet: -2.50 (0.63), residues: 62 loop : -0.99 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 144 HIS 0.006 0.001 HIS S 64 PHE 0.034 0.001 PHE D 211 TYR 0.023 0.001 TYR C 42 ARG 0.011 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 936) hydrogen bonds : angle 3.47178 ( 2760) covalent geometry : bond 0.00300 (13807) covalent geometry : angle 0.53112 (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 310 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 1.492 Fit side-chains REVERT: C 44 GLU cc_start: 0.7451 (pp20) cc_final: 0.6641 (pp20) REVERT: C 131 LYS cc_start: 0.8192 (tppp) cc_final: 0.7865 (tppp) REVERT: C 194 GLU cc_start: 0.7934 (mp0) cc_final: 0.7451 (mp0) REVERT: C 284 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7375 (tp40) REVERT: C 289 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7552 (ttp-170) REVERT: C 292 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7876 (mt-10) REVERT: C 485 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 641 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8235 (tp40) REVERT: C 648 LEU cc_start: 0.8259 (mp) cc_final: 0.8014 (tt) REVERT: C 751 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7547 (ttmm) REVERT: C 754 ASP cc_start: 0.8016 (t70) cc_final: 0.7682 (t0) REVERT: D 104 ASP cc_start: 0.7937 (t70) cc_final: 0.7533 (m-30) REVERT: D 306 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8595 (p) REVERT: D 341 ASP cc_start: 0.8120 (p0) cc_final: 0.7809 (p0) REVERT: D 366 GLU cc_start: 0.7668 (mp0) cc_final: 0.7372 (mp0) REVERT: D 534 LYS cc_start: 0.7966 (mttp) cc_final: 0.7726 (mttp) REVERT: D 706 MET cc_start: 0.8069 (tpt) cc_final: 0.7721 (mmm) REVERT: D 757 ASP cc_start: 0.7601 (m-30) cc_final: 0.7286 (m-30) REVERT: S 65 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.5945 (t-90) outliers start: 28 outliers final: 21 residues processed: 298 average time/residue: 0.2554 time to fit residues: 109.4209 Evaluate side-chains 301 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 537 ILE 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 179 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 185 THR 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 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 65 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 49 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.4268 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.142669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112452 restraints weight = 22499.934| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.00 r_work: 0.3242 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13807 Z= 0.111 Angle : 0.521 11.509 18877 Z= 0.263 Chirality : 0.038 0.152 2377 Planarity : 0.004 0.050 2435 Dihedral : 3.378 17.887 2076 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.09 % Allowed : 18.82 % Favored : 79.09 % 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: 1.92 (0.20), residues: 1957 helix: 2.34 (0.14), residues: 1338 sheet: -2.44 (0.66), residues: 60 loop : -0.99 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 144 HIS 0.004 0.001 HIS S 65 PHE 0.034 0.001 PHE D 211 TYR 0.021 0.001 TYR C 42 ARG 0.011 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 936) hydrogen bonds : angle 3.35352 ( 2760) covalent geometry : bond 0.00246 (13807) covalent geometry : angle 0.52145 (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 313 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 1.506 Fit side-chains REVERT: C 131 LYS cc_start: 0.8166 (tppp) cc_final: 0.7852 (tppp) REVERT: C 190 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 194 GLU cc_start: 0.7928 (mp0) cc_final: 0.7539 (mp0) REVERT: C 284 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7191 (tp40) REVERT: C 289 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7640 (ttp-170) REVERT: C 478 ASN cc_start: 0.8402 (p0) cc_final: 0.8137 (p0) REVERT: C 641 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8241 (tp40) REVERT: C 751 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7542 (ttmm) REVERT: C 754 ASP cc_start: 0.8005 (t70) cc_final: 0.7668 (t0) REVERT: D 12 LEU cc_start: 0.8485 (mm) cc_final: 0.8273 (mp) REVERT: D 104 ASP cc_start: 0.7919 (t70) cc_final: 0.7584 (m-30) REVERT: D 306 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (p) REVERT: D 341 ASP cc_start: 0.8113 (p0) cc_final: 0.7807 (p0) REVERT: D 366 GLU cc_start: 0.7618 (mp0) cc_final: 0.7316 (mp0) REVERT: D 757 ASP cc_start: 0.7544 (m-30) cc_final: 0.7242 (m-30) REVERT: S 65 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.5932 (t-90) outliers start: 24 outliers final: 17 residues processed: 303 average time/residue: 0.2675 time to fit residues: 115.6970 Evaluate side-chains 304 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 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 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 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 65 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 62 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112550 restraints weight = 22727.727| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.01 r_work: 0.3243 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 13807 Z= 0.174 Angle : 0.774 59.159 18877 Z= 0.442 Chirality : 0.038 0.149 2377 Planarity : 0.004 0.050 2435 Dihedral : 3.378 17.926 2076 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 19.25 % Favored : 78.75 % Cbeta Deviations : 0.05 % 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: 1.92 (0.20), residues: 1957 helix: 2.34 (0.14), residues: 1339 sheet: -2.44 (0.66), residues: 60 loop : -1.00 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 144 HIS 0.004 0.001 HIS S 65 PHE 0.032 0.001 PHE D 211 TYR 0.020 0.001 TYR C 42 ARG 0.011 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 936) hydrogen bonds : angle 3.35451 ( 2760) covalent geometry : bond 0.00340 (13807) covalent geometry : angle 0.77427 (18877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8220.52 seconds wall clock time: 142 minutes 19.71 seconds (8539.71 seconds total)