Starting phenix.real_space_refine on Sat Sep 12 23:52:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b5v_7058/09_2026/6b5v_7058.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 140 5.16 5 Cl 12 4.86 5 C 12276 2.51 5 N 3188 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18933 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "B" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "D" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "C" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4709 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 23, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, 'ECL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ECL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.23 Number of scatterers: 18933 At special positions: 0 Unit cell: (128.7, 128.7, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 12 17.00 S 140 16.00 O 3316 8.00 N 3188 7.00 C 12276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 832.9 milliseconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 4 sheets defined 57.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.633A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 removed outlier: 4.494A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.071A pdb=" N ALA A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.814A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 81 through 87 removed outlier: 4.277A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 removed outlier: 4.471A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 98' Processing helix chain 'A' and resid 102 through 107 removed outlier: 4.337A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.820A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 4.162A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 139' Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 184' Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.710A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.757A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 4.251A pdb=" N GLU A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.587A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 removed outlier: 3.706A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 removed outlier: 4.311A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.776A pdb=" N TYR A 467 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 468 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 464 through 471' Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 4.582A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 495' Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 37 through 47 removed outlier: 4.495A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.071A pdb=" N ALA B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.815A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 68' Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 4.472A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 98' Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.338A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.772A pdb=" N ILE B 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 4.161A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 139' Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 184' Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.711A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.756A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 removed outlier: 4.251A pdb=" N GLU B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 removed outlier: 3.706A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 4.312A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.775A pdb=" N TYR B 467 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 468 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 471' Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 4.583A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 495' Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 3.569A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 37 through 47 removed outlier: 4.494A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.070A pdb=" N ALA D 53 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.814A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 68' Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 4.471A pdb=" N LEU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.337A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.162A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 139' Processing helix chain 'D' and resid 149 through 153 removed outlier: 4.112A pdb=" N ARG D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.778A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 184' Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.709A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 4.214A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.757A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.857A pdb=" N CYS D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 347 removed outlier: 3.546A pdb=" N TYR D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS D 347 " --> pdb=" O PHE D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 397 removed outlier: 4.252A pdb=" N GLU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 removed outlier: 3.707A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 4.312A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.776A pdb=" N TYR D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 468 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 464 through 471' Processing helix chain 'D' and resid 477 through 487 removed outlier: 3.793A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 495 removed outlier: 4.583A pdb=" N PHE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 495' Processing helix chain 'D' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 537 removed outlier: 3.713A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 removed outlier: 3.980A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 removed outlier: 3.916A pdb=" N VAL D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.495A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.070A pdb=" N ALA C 53 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.815A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 68' Processing helix chain 'C' and resid 81 through 87 removed outlier: 4.276A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 removed outlier: 4.472A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 93 through 98' Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.338A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.819A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.771A pdb=" N ILE C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 removed outlier: 4.161A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 139' Processing helix chain 'C' and resid 149 through 153 removed outlier: 4.113A pdb=" N ARG C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.777A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.526A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 184' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.710A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 4.215A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.839A pdb=" N PHE C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.757A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.858A pdb=" N CYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 347 removed outlier: 3.547A pdb=" N TYR C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 removed outlier: 4.252A pdb=" N GLU C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.586A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 removed outlier: 3.707A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 436 " --> pdb=" O TYR C 432 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 removed outlier: 4.311A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.777A pdb=" N TYR C 467 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 468 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 464 through 471' Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.794A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 495 removed outlier: 4.582A pdb=" N PHE C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 495' Processing helix chain 'C' and resid 497 through 513 removed outlier: 3.503A pdb=" N ILE C 501 " --> pdb=" O MET C 497 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.712A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.570A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.979A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 592 removed outlier: 4.170A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.917A pdb=" N VAL C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.782A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 635 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.783A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 635 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.783A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 635 " --> pdb=" O THR D 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.782A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 635 " --> pdb=" O THR C 274 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5999 1.34 - 1.46: 4556 1.46 - 1.58: 8589 1.58 - 1.70: 4 1.70 - 1.82: 240 Bond restraints: 19388 Sorted by residual: bond pdb=" C11 ECL B1001 " pdb=" C9 ECL B1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C11 ECL C1001 " pdb=" C9 ECL C1001 " ideal model delta sigma weight residual 1.384 1.526 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL D1001 " pdb=" C2 ECL D1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C13 ECL A1001 " pdb=" C2 ECL A1001 " ideal model delta sigma weight residual 1.385 1.527 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C11 ECL A1001 " pdb=" C9 ECL A1001 " ideal model delta sigma weight residual 1.384 1.525 -0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 19383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24601 2.09 - 4.19: 1268 4.19 - 6.28: 284 6.28 - 8.38: 119 8.38 - 10.47: 52 Bond angle restraints: 26324 Sorted by residual: angle pdb=" N ARG D 584 " pdb=" CA ARG D 584 " pdb=" C ARG D 584 " ideal model delta sigma weight residual 111.07 120.47 -9.40 1.07e+00 8.73e-01 7.71e+01 angle pdb=" N ARG B 584 " pdb=" CA ARG B 584 " pdb=" C ARG B 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG A 584 " pdb=" CA ARG A 584 " pdb=" C ARG A 584 " ideal model delta sigma weight residual 111.07 120.45 -9.38 1.07e+00 8.73e-01 7.69e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.07 120.44 -9.37 1.07e+00 8.73e-01 7.66e+01 angle pdb=" C MET A 608 " pdb=" N PRO A 609 " pdb=" CA PRO A 609 " ideal model delta sigma weight residual 119.78 126.56 -6.78 1.03e+00 9.43e-01 4.33e+01 ... (remaining 26319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 9965 14.38 - 28.76: 1035 28.76 - 43.15: 336 43.15 - 57.53: 96 57.53 - 71.91: 36 Dihedral angle restraints: 11468 sinusoidal: 4592 harmonic: 6876 Sorted by residual: dihedral pdb=" CA LEU B 88 " pdb=" C LEU B 88 " pdb=" N TYR B 89 " pdb=" CA TYR B 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU A 88 " pdb=" C LEU A 88 " pdb=" N TYR A 89 " pdb=" CA TYR A 89 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU D 88 " pdb=" C LEU D 88 " pdb=" N TYR D 89 " pdb=" CA TYR D 89 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 11465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1894 0.048 - 0.095: 765 0.095 - 0.143: 241 0.143 - 0.191: 68 0.191 - 0.238: 16 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA ARG A 584 " pdb=" N ARG A 584 " pdb=" C ARG A 584 " pdb=" CB ARG A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG B 584 " pdb=" N ARG B 584 " pdb=" C ARG B 584 " pdb=" CB ARG B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG C 584 " pdb=" N ARG C 584 " pdb=" C ARG C 584 " pdb=" CB ARG C 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2981 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 517 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 516 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 516 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 517 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " -0.035 5.00e-02 4.00e+02 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 6163 2.85 - 3.36: 17528 3.36 - 3.87: 29314 3.87 - 4.39: 32057 4.39 - 4.90: 51670 Nonbonded interactions: 136732 Sorted by model distance: nonbonded pdb=" O LYS C 54 " pdb=" OH TYR C 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 54 " pdb=" OH TYR A 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS B 54 " pdb=" OH TYR B 89 " model vdw 2.333 3.040 nonbonded pdb=" O LYS D 54 " pdb=" OH TYR D 89 " model vdw 2.334 3.040 nonbonded pdb=" O GLY B 422 " pdb=" OH TYR B 467 " model vdw 2.368 3.040 ... (remaining 136727 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 1001) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.490 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.520 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.008 0.142 19388 Z= 0.395 Angle : 1.235 10.471 26324 Z= 0.654 Chirality : 0.059 0.238 2984 Planarity : 0.008 0.064 3316 Dihedral : 14.290 71.912 7028 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.55 % Allowed : 14.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.14), residues: 2340 helix: -4.04 (0.10), residues: 936 sheet: -0.18 (0.67), residues: 56 loop : -2.72 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 385 TYR 0.025 0.002 TYR B 278 PHE 0.029 0.002 PHE C 574 TRP 0.023 0.002 TRP B 629 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.40 (19388) covalent geometry : angle 1.23456 / 0.65 (26324) hydrogen bonds : bond 0.22062 / 14.65 ( 484) hydrogen bonds : angle 7.77524 / 5.25 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 599 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.9034 (ttp) cc_final: 0.8753 (ppp) REVERT: A 252 ASN cc_start: 0.9223 (t0) cc_final: 0.9005 (t0) REVERT: A 302 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7368 (ttt180) REVERT: A 386 LEU cc_start: 0.8988 (tm) cc_final: 0.8626 (mt) REVERT: A 403 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7775 (tp30) REVERT: A 491 MET cc_start: 0.7160 (ttm) cc_final: 0.6956 (tmm) REVERT: A 509 HIS cc_start: 0.9077 (t70) cc_final: 0.8740 (t70) REVERT: A 603 MET cc_start: 0.8640 (tmt) cc_final: 0.8227 (tmm) REVERT: A 616 SER cc_start: 0.9293 (p) cc_final: 0.9022 (t) REVERT: B 326 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7711 (mmm-85) REVERT: B 386 LEU cc_start: 0.9132 (tm) cc_final: 0.8798 (mt) REVERT: B 403 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7923 (tp30) REVERT: B 509 HIS cc_start: 0.9059 (t70) cc_final: 0.8727 (t70) REVERT: B 535 GLU cc_start: 0.8201 (pp20) cc_final: 0.7917 (pp20) REVERT: B 578 MET cc_start: 0.9098 (tmt) cc_final: 0.8822 (tmm) REVERT: B 632 ARG cc_start: 0.8755 (ttp-170) cc_final: 0.8324 (tmm-80) REVERT: D 42 GLU cc_start: 0.8834 (pm20) cc_final: 0.8599 (pm20) REVERT: D 59 ARG cc_start: 0.8033 (tmm160) cc_final: 0.7576 (ttp80) REVERT: D 252 ASN cc_start: 0.9293 (t0) cc_final: 0.9083 (t0) REVERT: D 302 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7314 (ttt180) REVERT: D 309 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 326 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7772 (mmm-85) REVERT: D 386 LEU cc_start: 0.8813 (tm) cc_final: 0.8402 (mt) REVERT: D 403 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7772 (tp30) REVERT: D 442 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: D 497 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (tpt) REVERT: D 509 HIS cc_start: 0.9108 (t70) cc_final: 0.8837 (t70) REVERT: D 520 LEU cc_start: 0.8202 (tp) cc_final: 0.7993 (tt) REVERT: D 535 GLU cc_start: 0.8237 (pp20) cc_final: 0.7946 (pp20) REVERT: D 562 PHE cc_start: 0.9263 (t80) cc_final: 0.9036 (t80) REVERT: D 603 MET cc_start: 0.8629 (tmt) cc_final: 0.8236 (tmm) REVERT: D 616 SER cc_start: 0.9232 (p) cc_final: 0.8788 (t) REVERT: C 42 GLU cc_start: 0.8833 (pm20) cc_final: 0.8588 (pm20) REVERT: C 59 ARG cc_start: 0.8060 (tmm160) cc_final: 0.7679 (ttp80) REVERT: C 260 MET cc_start: 0.8662 (mmp) cc_final: 0.8451 (mmp) REVERT: C 302 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7308 (ttt180) REVERT: C 386 LEU cc_start: 0.9108 (tm) cc_final: 0.8774 (mt) REVERT: C 403 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 497 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (ttm) REVERT: C 509 HIS cc_start: 0.9066 (t70) cc_final: 0.8744 (t70) REVERT: C 535 GLU cc_start: 0.8262 (pp20) cc_final: 0.8014 (pp20) REVERT: C 603 MET cc_start: 0.8637 (tmt) cc_final: 0.8236 (tmm) outliers start: 72 outliers final: 17 residues processed: 634 average time/residue: 0.1575 time to fit residues: 148.6694 Evaluate side-chains 452 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 432 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.0374 > 50:) chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 84 HIS A 118 GLN A 129 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 73 GLN B 118 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN D 73 GLN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN C 73 GLN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092961 restraints weight = 50687.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095771 restraints weight = 34697.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097901 restraints weight = 25697.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099580 restraints weight = 20102.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100907 restraints weight = 16373.276| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19388 Z= 0.112 Angle : 0.714 8.032 26324 Z= 0.348 Chirality : 0.044 0.163 2984 Planarity : 0.005 0.045 3316 Dihedral : 7.513 59.904 2612 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.15), residues: 2340 helix: -3.05 (0.13), residues: 980 sheet: 0.21 (0.62), residues: 56 loop : -2.25 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 35 TYR 0.014 0.001 TYR B 89 PHE 0.028 0.001 PHE A 408 TRP 0.018 0.001 TRP D 583 HIS 0.003 0.000 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (19388) covalent geometry : angle 0.71409 / 0.35 (26324) hydrogen bonds : bond 0.03675 / 2.42 ( 484) hydrogen bonds : angle 4.71579 / 3.21 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8765 (t0) cc_final: 0.8367 (t0) REVERT: A 178 ILE cc_start: 0.8867 (pt) cc_final: 0.8650 (tp) REVERT: A 181 LEU cc_start: 0.9356 (tt) cc_final: 0.9145 (mm) REVERT: A 303 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 340 MET cc_start: 0.9155 (ttm) cc_final: 0.8738 (ttm) REVERT: A 386 LEU cc_start: 0.9215 (tt) cc_final: 0.8694 (mt) REVERT: A 403 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7235 (tp30) REVERT: A 497 MET cc_start: 0.7753 (ttt) cc_final: 0.7222 (ttt) REVERT: A 509 HIS cc_start: 0.8668 (t70) cc_final: 0.8335 (t-170) REVERT: A 577 MET cc_start: 0.7500 (tpt) cc_final: 0.7262 (tpt) REVERT: A 632 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8301 (tmm-80) REVERT: B 126 MET cc_start: 0.8243 (ppp) cc_final: 0.8034 (ppp) REVERT: B 178 ILE cc_start: 0.8807 (pt) cc_final: 0.8569 (tp) REVERT: B 294 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 302 ARG cc_start: 0.8406 (mmt180) cc_final: 0.7523 (ttt180) REVERT: B 386 LEU cc_start: 0.9264 (tt) cc_final: 0.8723 (mt) REVERT: B 403 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7309 (tp30) REVERT: B 438 LEU cc_start: 0.8931 (tt) cc_final: 0.8725 (pp) REVERT: B 447 MET cc_start: 0.6567 (ttt) cc_final: 0.6338 (tpp) REVERT: B 497 MET cc_start: 0.7777 (ttt) cc_final: 0.6913 (tmm) REVERT: B 509 HIS cc_start: 0.8619 (t70) cc_final: 0.8367 (t70) REVERT: B 577 MET cc_start: 0.7501 (tpt) cc_final: 0.7198 (tpt) REVERT: B 632 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8074 (tmm-80) REVERT: D 178 ILE cc_start: 0.8834 (pt) cc_final: 0.8629 (tp) REVERT: D 302 ARG cc_start: 0.8413 (mmt180) cc_final: 0.7563 (ttt180) REVERT: D 303 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8387 (tm-30) REVERT: D 335 LEU cc_start: 0.9024 (mp) cc_final: 0.8641 (tt) REVERT: D 386 LEU cc_start: 0.9091 (tt) cc_final: 0.8421 (mt) REVERT: D 497 MET cc_start: 0.7713 (ttt) cc_final: 0.6995 (tmm) REVERT: D 501 ILE cc_start: 0.9558 (pt) cc_final: 0.9295 (pt) REVERT: D 509 HIS cc_start: 0.8544 (t70) cc_final: 0.8330 (t70) REVERT: D 554 MET cc_start: 0.8409 (mmm) cc_final: 0.8164 (tpt) REVERT: D 562 PHE cc_start: 0.8866 (t80) cc_final: 0.8627 (t80) REVERT: D 577 MET cc_start: 0.8378 (tpt) cc_final: 0.8050 (tpt) REVERT: D 616 SER cc_start: 0.9004 (p) cc_final: 0.8726 (t) REVERT: C 178 ILE cc_start: 0.8831 (pt) cc_final: 0.8619 (tp) REVERT: C 200 LEU cc_start: 0.9519 (mp) cc_final: 0.8870 (tp) REVERT: C 302 ARG cc_start: 0.8446 (mmt180) cc_final: 0.7624 (ttt180) REVERT: C 340 MET cc_start: 0.9210 (ttm) cc_final: 0.8964 (ttm) REVERT: C 386 LEU cc_start: 0.9257 (tt) cc_final: 0.8740 (mt) REVERT: C 403 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7160 (tp30) REVERT: C 491 MET cc_start: 0.6621 (ttm) cc_final: 0.6413 (ttm) REVERT: C 497 MET cc_start: 0.7732 (ttt) cc_final: 0.6941 (tmm) REVERT: C 509 HIS cc_start: 0.8549 (t70) cc_final: 0.8310 (t70) REVERT: C 577 MET cc_start: 0.8313 (tpt) cc_final: 0.7978 (tpt) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.1368 time to fit residues: 120.1048 Evaluate side-chains 421 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 58 optimal weight: 10.0000 chunk 157 optimal weight: 0.4980 chunk 160 optimal weight: 0.0010 chunk 54 optimal weight: 10.0000 chunk 185 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 overall best weight: 2.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 165 HIS A 426 HIS A 513 GLN B 41 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 165 HIS B 426 HIS B 513 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 129 ASN D 165 HIS D 426 HIS D 513 GLN C 84 HIS C 129 ASN C 165 HIS C 426 HIS C 513 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083749 restraints weight = 53274.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086390 restraints weight = 35831.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088367 restraints weight = 26214.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089878 restraints weight = 20363.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091013 restraints weight = 16529.887| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19388 Z= 0.146 Angle : 0.714 8.392 26324 Z= 0.355 Chirality : 0.045 0.166 2984 Planarity : 0.004 0.082 3316 Dihedral : 7.043 56.386 2612 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.16), residues: 2340 helix: -2.31 (0.14), residues: 1016 sheet: 0.56 (0.63), residues: 56 loop : -2.02 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 326 TYR 0.017 0.002 TYR D 547 PHE 0.026 0.002 PHE B 408 TRP 0.010 0.002 TRP A 629 HIS 0.007 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (19388) covalent geometry : angle 0.71373 / 0.35 (26324) hydrogen bonds : bond 0.03673 / 2.44 ( 484) hydrogen bonds : angle 4.48523 / 3.08 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7585 (ttp80) REVERT: A 159 LEU cc_start: 0.7929 (tp) cc_final: 0.7721 (tt) REVERT: A 303 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8363 (tm-30) REVERT: A 403 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7320 (tp30) REVERT: A 485 MET cc_start: 0.8896 (ppp) cc_final: 0.7990 (ptm) REVERT: A 497 MET cc_start: 0.7996 (ttt) cc_final: 0.7214 (tmm) REVERT: A 501 ILE cc_start: 0.9596 (pt) cc_final: 0.9064 (pt) REVERT: A 509 HIS cc_start: 0.8788 (t70) cc_final: 0.8348 (t-170) REVERT: A 632 ARG cc_start: 0.8960 (ttp-170) cc_final: 0.8721 (tmm-80) REVERT: B 178 ILE cc_start: 0.8955 (pt) cc_final: 0.8697 (tp) REVERT: B 266 VAL cc_start: 0.9430 (t) cc_final: 0.9186 (t) REVERT: B 294 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 403 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7177 (tp30) REVERT: B 438 LEU cc_start: 0.8962 (tt) cc_final: 0.8729 (mm) REVERT: B 497 MET cc_start: 0.7909 (ttt) cc_final: 0.7170 (tmm) REVERT: B 501 ILE cc_start: 0.9609 (pt) cc_final: 0.9113 (pt) REVERT: B 509 HIS cc_start: 0.8718 (t70) cc_final: 0.8378 (t-170) REVERT: B 632 ARG cc_start: 0.8955 (ttp-170) cc_final: 0.8505 (tmm-80) REVERT: D 34 ASP cc_start: 0.9134 (t0) cc_final: 0.8772 (t0) REVERT: D 38 MET cc_start: 0.8716 (pmm) cc_final: 0.8338 (pmm) REVERT: D 99 MET cc_start: 0.8989 (mpp) cc_final: 0.8391 (mpp) REVERT: D 178 ILE cc_start: 0.8935 (pt) cc_final: 0.8712 (tp) REVERT: D 303 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8137 (tm-30) REVERT: D 335 LEU cc_start: 0.9139 (mp) cc_final: 0.8745 (tt) REVERT: D 485 MET cc_start: 0.8942 (ppp) cc_final: 0.8126 (ptm) REVERT: D 497 MET cc_start: 0.7872 (ttt) cc_final: 0.7092 (tmm) REVERT: D 501 ILE cc_start: 0.9663 (pt) cc_final: 0.9151 (pt) REVERT: D 509 HIS cc_start: 0.8690 (t70) cc_final: 0.8267 (t70) REVERT: D 577 MET cc_start: 0.8432 (tpt) cc_final: 0.8010 (tpt) REVERT: D 604 LEU cc_start: 0.9058 (tt) cc_final: 0.8828 (tt) REVERT: D 632 ARG cc_start: 0.8922 (ttp-170) cc_final: 0.8537 (tmm-80) REVERT: C 59 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7731 (ttp80) REVERT: C 99 MET cc_start: 0.8973 (mpp) cc_final: 0.8399 (mpp) REVERT: C 159 LEU cc_start: 0.7933 (tp) cc_final: 0.7693 (tt) REVERT: C 178 ILE cc_start: 0.8944 (pt) cc_final: 0.8706 (tp) REVERT: C 200 LEU cc_start: 0.9559 (mp) cc_final: 0.9358 (mm) REVERT: C 303 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 310 GLN cc_start: 0.8428 (tp40) cc_final: 0.8209 (tp40) REVERT: C 403 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7323 (tp30) REVERT: C 442 MET cc_start: 0.8379 (tmm) cc_final: 0.7997 (tmm) REVERT: C 485 MET cc_start: 0.8926 (ppp) cc_final: 0.8075 (ptm) REVERT: C 497 MET cc_start: 0.7924 (ttt) cc_final: 0.7185 (tmm) REVERT: C 501 ILE cc_start: 0.9618 (pt) cc_final: 0.9131 (pt) REVERT: C 509 HIS cc_start: 0.8710 (t70) cc_final: 0.8354 (t-170) REVERT: C 577 MET cc_start: 0.8399 (tpt) cc_final: 0.8141 (tpt) REVERT: C 604 LEU cc_start: 0.9002 (tt) cc_final: 0.8766 (tt) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.1305 time to fit residues: 100.0863 Evaluate side-chains 359 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 231 optimal weight: 10.0000 chunk 220 optimal weight: 0.0370 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 513 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN D 84 HIS D 513 GLN C 84 HIS C 513 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079765 restraints weight = 54553.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082339 restraints weight = 36050.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084234 restraints weight = 26147.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085706 restraints weight = 20262.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086777 restraints weight = 16429.522| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19388 Z= 0.148 Angle : 0.707 7.384 26324 Z= 0.347 Chirality : 0.044 0.157 2984 Planarity : 0.004 0.059 3316 Dihedral : 6.776 54.737 2612 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.17), residues: 2340 helix: -1.82 (0.15), residues: 1040 sheet: 0.87 (0.67), residues: 56 loop : -1.70 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 326 TYR 0.013 0.002 TYR D 547 PHE 0.031 0.002 PHE B 574 TRP 0.010 0.001 TRP C 593 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (19388) covalent geometry : angle 0.70734 / 0.35 (26324) hydrogen bonds : bond 0.03320 / 2.21 ( 484) hydrogen bonds : angle 4.45532 / 3.07 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7538 (ttp80) REVERT: A 159 LEU cc_start: 0.7984 (tp) cc_final: 0.7733 (tt) REVERT: A 403 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7196 (tp30) REVERT: A 430 ILE cc_start: 0.9377 (pt) cc_final: 0.9093 (mm) REVERT: A 482 ILE cc_start: 0.9239 (pt) cc_final: 0.9009 (pt) REVERT: A 485 MET cc_start: 0.8820 (ppp) cc_final: 0.8038 (ttp) REVERT: A 497 MET cc_start: 0.8295 (ttt) cc_final: 0.7468 (tmm) REVERT: A 501 ILE cc_start: 0.9637 (pt) cc_final: 0.8954 (pt) REVERT: A 509 HIS cc_start: 0.8779 (t70) cc_final: 0.8437 (t70) REVERT: A 604 LEU cc_start: 0.8986 (tt) cc_final: 0.8768 (tt) REVERT: A 632 ARG cc_start: 0.8895 (ttp-170) cc_final: 0.8461 (tmm-80) REVERT: B 80 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8856 (mp0) REVERT: B 178 ILE cc_start: 0.9001 (pt) cc_final: 0.8779 (tp) REVERT: B 200 LEU cc_start: 0.9525 (mp) cc_final: 0.9290 (mm) REVERT: B 294 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 403 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7254 (tp30) REVERT: B 430 ILE cc_start: 0.9368 (pt) cc_final: 0.9079 (mm) REVERT: B 439 THR cc_start: 0.9093 (p) cc_final: 0.8782 (p) REVERT: B 442 MET cc_start: 0.8335 (tmm) cc_final: 0.7998 (tmm) REVERT: B 485 MET cc_start: 0.8612 (ppp) cc_final: 0.8181 (ttp) REVERT: B 497 MET cc_start: 0.8299 (ttt) cc_final: 0.7604 (tmm) REVERT: B 501 ILE cc_start: 0.9658 (pt) cc_final: 0.9038 (pt) REVERT: B 509 HIS cc_start: 0.8683 (t70) cc_final: 0.8322 (t70) REVERT: B 535 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 603 MET cc_start: 0.8796 (tmm) cc_final: 0.8537 (tmm) REVERT: B 632 ARG cc_start: 0.8936 (ttp-170) cc_final: 0.8576 (tmm-80) REVERT: D 38 MET cc_start: 0.8761 (pmm) cc_final: 0.8519 (pmm) REVERT: D 80 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8834 (mp0) REVERT: D 99 MET cc_start: 0.8903 (mpp) cc_final: 0.8366 (mpp) REVERT: D 127 ASN cc_start: 0.8840 (p0) cc_final: 0.8558 (p0) REVERT: D 176 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7355 (mp0) REVERT: D 200 LEU cc_start: 0.9553 (mp) cc_final: 0.9329 (mm) REVERT: D 303 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8186 (tm-30) REVERT: D 310 GLN cc_start: 0.8659 (tp40) cc_final: 0.8262 (tp40) REVERT: D 335 LEU cc_start: 0.9171 (mp) cc_final: 0.8747 (tt) REVERT: D 497 MET cc_start: 0.8370 (ttt) cc_final: 0.7676 (tmm) REVERT: D 501 ILE cc_start: 0.9668 (pt) cc_final: 0.8980 (pt) REVERT: D 509 HIS cc_start: 0.8700 (t70) cc_final: 0.8302 (t70) REVERT: D 577 MET cc_start: 0.8392 (tpt) cc_final: 0.8000 (tpt) REVERT: D 632 ARG cc_start: 0.8885 (ttp-170) cc_final: 0.8541 (tmm-80) REVERT: C 38 MET cc_start: 0.8745 (pmm) cc_final: 0.8474 (pmm) REVERT: C 59 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7360 (ttp80) REVERT: C 80 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8831 (mp0) REVERT: C 99 MET cc_start: 0.8862 (mpp) cc_final: 0.8342 (mpp) REVERT: C 127 ASN cc_start: 0.8853 (p0) cc_final: 0.8559 (p0) REVERT: C 159 LEU cc_start: 0.8022 (tp) cc_final: 0.7802 (tt) REVERT: C 200 LEU cc_start: 0.9548 (mp) cc_final: 0.9333 (mm) REVERT: C 294 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 310 GLN cc_start: 0.8533 (tp40) cc_final: 0.8158 (tp40) REVERT: C 340 MET cc_start: 0.9286 (ttt) cc_final: 0.8870 (ttm) REVERT: C 403 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7272 (tp30) REVERT: C 430 ILE cc_start: 0.9363 (pt) cc_final: 0.9047 (mm) REVERT: C 485 MET cc_start: 0.8745 (ppp) cc_final: 0.8229 (ttm) REVERT: C 497 MET cc_start: 0.8365 (ttt) cc_final: 0.7713 (tmm) REVERT: C 501 ILE cc_start: 0.9661 (pt) cc_final: 0.9046 (pt) REVERT: C 509 HIS cc_start: 0.8712 (t70) cc_final: 0.8376 (t70) REVERT: C 577 MET cc_start: 0.8245 (tpt) cc_final: 0.7937 (tpt) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1331 time to fit residues: 98.5887 Evaluate side-chains 347 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 207 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 310 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.073556 restraints weight = 56656.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.075976 restraints weight = 36410.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077793 restraints weight = 26211.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079077 restraints weight = 20038.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080142 restraints weight = 16308.051| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19388 Z= 0.217 Angle : 0.785 9.021 26324 Z= 0.395 Chirality : 0.047 0.161 2984 Planarity : 0.005 0.054 3316 Dihedral : 7.301 54.616 2612 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.17), residues: 2340 helix: -1.47 (0.15), residues: 984 sheet: 0.84 (0.67), residues: 56 loop : -1.49 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 632 TYR 0.022 0.002 TYR B 328 PHE 0.035 0.002 PHE B 574 TRP 0.017 0.002 TRP C 593 HIS 0.007 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (19388) covalent geometry : angle 0.78459 / 0.39 (26324) hydrogen bonds : bond 0.03811 / 2.50 ( 484) hydrogen bonds : angle 5.10530 / 3.54 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7562 (ttp80) REVERT: A 99 MET cc_start: 0.8703 (mpp) cc_final: 0.8277 (mpp) REVERT: A 303 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8252 (tp30) REVERT: A 403 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7392 (tp30) REVERT: A 404 ILE cc_start: 0.9091 (tt) cc_final: 0.8871 (pt) REVERT: A 497 MET cc_start: 0.8558 (ttt) cc_final: 0.7675 (tmm) REVERT: A 501 ILE cc_start: 0.9647 (pt) cc_final: 0.8806 (pt) REVERT: A 509 HIS cc_start: 0.8681 (t70) cc_final: 0.8257 (t70) REVERT: A 535 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 99 MET cc_start: 0.8675 (mpp) cc_final: 0.8147 (mpp) REVERT: B 178 ILE cc_start: 0.9139 (pt) cc_final: 0.8909 (tp) REVERT: B 200 LEU cc_start: 0.9525 (mp) cc_final: 0.9300 (mm) REVERT: B 245 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9094 (mmmm) REVERT: B 260 MET cc_start: 0.9138 (mmp) cc_final: 0.8738 (mmt) REVERT: B 303 GLU cc_start: 0.8860 (pt0) cc_final: 0.8509 (pp20) REVERT: B 403 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7358 (tp30) REVERT: B 442 MET cc_start: 0.8541 (tmm) cc_final: 0.8218 (tmm) REVERT: B 482 ILE cc_start: 0.9393 (tt) cc_final: 0.9157 (tt) REVERT: B 497 MET cc_start: 0.8638 (ttt) cc_final: 0.7712 (tmm) REVERT: B 501 ILE cc_start: 0.9687 (pt) cc_final: 0.8653 (pt) REVERT: B 509 HIS cc_start: 0.8644 (t70) cc_final: 0.8267 (t70) REVERT: D 34 ASP cc_start: 0.9111 (t0) cc_final: 0.8821 (t0) REVERT: D 38 MET cc_start: 0.8711 (pmm) cc_final: 0.8400 (pmm) REVERT: D 80 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8855 (mp0) REVERT: D 99 MET cc_start: 0.8742 (mpp) cc_final: 0.8344 (mpp) REVERT: D 335 LEU cc_start: 0.9245 (mp) cc_final: 0.8791 (tt) REVERT: D 442 MET cc_start: 0.8645 (tmm) cc_final: 0.8200 (tmm) REVERT: D 482 ILE cc_start: 0.9392 (pt) cc_final: 0.9104 (pt) REVERT: D 493 PHE cc_start: 0.8303 (t80) cc_final: 0.8097 (t80) REVERT: D 497 MET cc_start: 0.8627 (ttt) cc_final: 0.7722 (tmm) REVERT: D 501 ILE cc_start: 0.9659 (pt) cc_final: 0.8644 (pt) REVERT: D 509 HIS cc_start: 0.8718 (t70) cc_final: 0.8278 (t70) REVERT: C 59 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7514 (ttp80) REVERT: C 80 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8810 (mp0) REVERT: C 99 MET cc_start: 0.8713 (mpp) cc_final: 0.8342 (mpp) REVERT: C 200 LEU cc_start: 0.9496 (mp) cc_final: 0.9283 (mm) REVERT: C 260 MET cc_start: 0.9094 (mmp) cc_final: 0.8635 (mmt) REVERT: C 303 GLU cc_start: 0.8968 (pt0) cc_final: 0.8565 (pp20) REVERT: C 403 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7324 (tp30) REVERT: C 442 MET cc_start: 0.8569 (tmm) cc_final: 0.8356 (tmm) REVERT: C 482 ILE cc_start: 0.9395 (tt) cc_final: 0.9137 (tt) REVERT: C 497 MET cc_start: 0.8633 (ttt) cc_final: 0.7782 (tmm) REVERT: C 501 ILE cc_start: 0.9667 (pt) cc_final: 0.8756 (pt) REVERT: C 509 HIS cc_start: 0.8664 (t70) cc_final: 0.8270 (t70) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.1336 time to fit residues: 92.2448 Evaluate side-chains 349 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 222 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 140 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN B 74 GLN D 74 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.078097 restraints weight = 54413.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080557 restraints weight = 36274.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082356 restraints weight = 26376.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083706 restraints weight = 20481.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084739 restraints weight = 16649.708| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19388 Z= 0.111 Angle : 0.696 7.327 26324 Z= 0.333 Chirality : 0.044 0.152 2984 Planarity : 0.004 0.050 3316 Dihedral : 6.582 53.000 2612 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.20 % Allowed : 3.40 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.17), residues: 2340 helix: -1.43 (0.15), residues: 1024 sheet: 0.98 (0.66), residues: 56 loop : -1.38 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 443 TYR 0.010 0.001 TYR B 415 PHE 0.033 0.001 PHE C 574 TRP 0.008 0.001 TRP A 583 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (19388) covalent geometry : angle 0.69551 / 0.33 (26324) hydrogen bonds : bond 0.03131 / 2.09 ( 484) hydrogen bonds : angle 4.33593 / 2.97 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 476 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7595 (ttp80) REVERT: A 99 MET cc_start: 0.8734 (mpp) cc_final: 0.8260 (mpp) REVERT: A 250 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8996 (mm-30) REVERT: A 260 MET cc_start: 0.9080 (mmp) cc_final: 0.8696 (mmp) REVERT: A 340 MET cc_start: 0.9169 (ttm) cc_final: 0.8909 (ttm) REVERT: A 403 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7199 (tp30) REVERT: A 430 ILE cc_start: 0.9276 (pt) cc_final: 0.9048 (mm) REVERT: A 482 ILE cc_start: 0.9319 (pt) cc_final: 0.9110 (pt) REVERT: A 497 MET cc_start: 0.8676 (ttt) cc_final: 0.7654 (tmm) REVERT: A 501 ILE cc_start: 0.9587 (pt) cc_final: 0.8635 (pt) REVERT: A 509 HIS cc_start: 0.8607 (t70) cc_final: 0.8192 (t70) REVERT: A 535 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 536 LEU cc_start: 0.8566 (tt) cc_final: 0.8309 (tt) REVERT: A 572 ASN cc_start: 0.8171 (m110) cc_final: 0.7583 (m110) REVERT: B 99 MET cc_start: 0.8687 (mpp) cc_final: 0.8153 (mpp) REVERT: B 245 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9044 (mmmt) REVERT: B 260 MET cc_start: 0.9142 (mmp) cc_final: 0.8322 (mmm) REVERT: B 261 GLN cc_start: 0.8796 (mp10) cc_final: 0.8311 (mp10) REVERT: B 403 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7172 (tp30) REVERT: B 493 PHE cc_start: 0.8423 (t80) cc_final: 0.8196 (t80) REVERT: B 497 MET cc_start: 0.8607 (ttt) cc_final: 0.7571 (tmm) REVERT: B 501 ILE cc_start: 0.9601 (pt) cc_final: 0.8494 (pt) REVERT: B 509 HIS cc_start: 0.8535 (t70) cc_final: 0.8151 (t70) REVERT: B 535 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 572 ASN cc_start: 0.7971 (m110) cc_final: 0.7583 (m110) REVERT: B 603 MET cc_start: 0.8768 (tmm) cc_final: 0.8266 (tmm) REVERT: D 99 MET cc_start: 0.8760 (mpp) cc_final: 0.8347 (mpp) REVERT: D 260 MET cc_start: 0.9048 (mmp) cc_final: 0.8332 (mmm) REVERT: D 430 ILE cc_start: 0.9310 (pt) cc_final: 0.9077 (mm) REVERT: D 493 PHE cc_start: 0.8321 (t80) cc_final: 0.8072 (t80) REVERT: D 497 MET cc_start: 0.8675 (ttt) cc_final: 0.7749 (tmm) REVERT: D 501 ILE cc_start: 0.9560 (pt) cc_final: 0.8566 (pt) REVERT: D 509 HIS cc_start: 0.8567 (t70) cc_final: 0.8138 (t70) REVERT: D 535 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 572 ASN cc_start: 0.8258 (m110) cc_final: 0.7912 (m110) REVERT: D 577 MET cc_start: 0.8577 (tpt) cc_final: 0.8070 (tpt) REVERT: C 59 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7517 (ttp80) REVERT: C 99 MET cc_start: 0.8698 (mpp) cc_final: 0.8292 (mpp) REVERT: C 260 MET cc_start: 0.9042 (mmp) cc_final: 0.8614 (mmt) REVERT: C 310 GLN cc_start: 0.8578 (tp40) cc_final: 0.8289 (tp40) REVERT: C 403 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7269 (tp30) REVERT: C 430 ILE cc_start: 0.9278 (pt) cc_final: 0.9044 (mm) REVERT: C 439 THR cc_start: 0.9048 (p) cc_final: 0.8789 (p) REVERT: C 442 MET cc_start: 0.8585 (tmm) cc_final: 0.8356 (tmm) REVERT: C 493 PHE cc_start: 0.8343 (t80) cc_final: 0.8132 (t80) REVERT: C 497 MET cc_start: 0.8668 (ttt) cc_final: 0.7668 (tmm) REVERT: C 501 ILE cc_start: 0.9571 (pt) cc_final: 0.8530 (pt) REVERT: C 509 HIS cc_start: 0.8562 (t70) cc_final: 0.8156 (t70) outliers start: 4 outliers final: 0 residues processed: 480 average time/residue: 0.1282 time to fit residues: 97.1215 Evaluate side-chains 355 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 146 optimal weight: 9.9990 chunk 62 optimal weight: 0.0170 chunk 84 optimal weight: 0.2980 chunk 199 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 142 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078743 restraints weight = 54417.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.081220 restraints weight = 36303.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083047 restraints weight = 26379.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084367 restraints weight = 20475.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085437 restraints weight = 16784.247| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19388 Z= 0.109 Angle : 0.708 7.685 26324 Z= 0.334 Chirality : 0.044 0.150 2984 Planarity : 0.004 0.051 3316 Dihedral : 6.356 51.770 2612 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 2340 helix: -1.23 (0.16), residues: 1000 sheet: 1.05 (0.66), residues: 56 loop : -1.31 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 409 TYR 0.023 0.001 TYR B 328 PHE 0.029 0.001 PHE C 574 TRP 0.007 0.001 TRP B 286 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (19388) covalent geometry : angle 0.70786 / 0.33 (26324) hydrogen bonds : bond 0.03062 / 2.03 ( 484) hydrogen bonds : angle 4.11269 / 2.81 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7638 (ttp80) REVERT: A 80 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8573 (mp0) REVERT: A 99 MET cc_start: 0.8765 (mpp) cc_final: 0.8364 (mpp) REVERT: A 250 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 260 MET cc_start: 0.9124 (mmp) cc_final: 0.8801 (mmp) REVERT: A 303 GLU cc_start: 0.8813 (pt0) cc_final: 0.8587 (pp20) REVERT: A 403 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7136 (tp30) REVERT: A 493 PHE cc_start: 0.8430 (t80) cc_final: 0.8213 (t80) REVERT: A 497 MET cc_start: 0.8739 (ttt) cc_final: 0.7721 (tmm) REVERT: A 501 ILE cc_start: 0.9548 (pt) cc_final: 0.8542 (pt) REVERT: A 509 HIS cc_start: 0.8606 (t70) cc_final: 0.8229 (t-170) REVERT: A 536 LEU cc_start: 0.8565 (tt) cc_final: 0.8289 (tt) REVERT: A 572 ASN cc_start: 0.7974 (m110) cc_final: 0.7627 (m110) REVERT: B 99 MET cc_start: 0.8658 (mpp) cc_final: 0.8151 (mpp) REVERT: B 245 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9075 (mmmt) REVERT: B 252 ASN cc_start: 0.9091 (t0) cc_final: 0.8792 (t0) REVERT: B 260 MET cc_start: 0.9127 (mmp) cc_final: 0.8513 (mmm) REVERT: B 403 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7209 (tp30) REVERT: B 493 PHE cc_start: 0.8573 (t80) cc_final: 0.8253 (t80) REVERT: B 497 MET cc_start: 0.8748 (ttt) cc_final: 0.7736 (tmm) REVERT: B 501 ILE cc_start: 0.9578 (pt) cc_final: 0.8598 (pt) REVERT: B 509 HIS cc_start: 0.8577 (t70) cc_final: 0.8217 (t70) REVERT: B 535 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 603 MET cc_start: 0.8770 (tmm) cc_final: 0.8285 (tmm) REVERT: D 99 MET cc_start: 0.8723 (mpp) cc_final: 0.8305 (mpp) REVERT: D 260 MET cc_start: 0.9090 (mmp) cc_final: 0.8494 (mmm) REVERT: D 430 ILE cc_start: 0.9343 (pt) cc_final: 0.9072 (mm) REVERT: D 447 MET cc_start: 0.7739 (tpt) cc_final: 0.7331 (tpp) REVERT: D 485 MET cc_start: 0.7894 (tpp) cc_final: 0.7522 (ttt) REVERT: D 493 PHE cc_start: 0.8311 (t80) cc_final: 0.8094 (t80) REVERT: D 497 MET cc_start: 0.8733 (ttt) cc_final: 0.7798 (tmm) REVERT: D 501 ILE cc_start: 0.9561 (pt) cc_final: 0.8557 (pt) REVERT: D 509 HIS cc_start: 0.8620 (t70) cc_final: 0.8198 (t70) REVERT: D 535 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 572 ASN cc_start: 0.8344 (m110) cc_final: 0.7919 (m110) REVERT: C 59 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7478 (ttp80) REVERT: C 99 MET cc_start: 0.8688 (mpp) cc_final: 0.8330 (mpp) REVERT: C 260 MET cc_start: 0.9048 (mmp) cc_final: 0.8223 (mmm) REVERT: C 261 GLN cc_start: 0.8837 (mp10) cc_final: 0.8336 (mp10) REVERT: C 310 GLN cc_start: 0.8606 (tp40) cc_final: 0.8319 (tp40) REVERT: C 403 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7180 (tp30) REVERT: C 439 THR cc_start: 0.9031 (p) cc_final: 0.8801 (p) REVERT: C 442 MET cc_start: 0.8489 (tmm) cc_final: 0.8152 (tmm) REVERT: C 493 PHE cc_start: 0.8474 (t80) cc_final: 0.8199 (t80) REVERT: C 497 MET cc_start: 0.8681 (ttt) cc_final: 0.7723 (tmm) REVERT: C 501 ILE cc_start: 0.9573 (pt) cc_final: 0.8591 (pt) REVERT: C 509 HIS cc_start: 0.8580 (t70) cc_final: 0.8207 (t70) REVERT: C 572 ASN cc_start: 0.8109 (m110) cc_final: 0.7772 (m110) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1261 time to fit residues: 93.8919 Evaluate side-chains 366 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 149 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 112 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN D 74 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.096718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.077383 restraints weight = 54169.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080018 restraints weight = 35007.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081953 restraints weight = 25012.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083346 restraints weight = 19170.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084462 restraints weight = 15542.135| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19388 Z= 0.119 Angle : 0.718 9.154 26324 Z= 0.339 Chirality : 0.045 0.147 2984 Planarity : 0.004 0.049 3316 Dihedral : 6.314 50.695 2612 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.15 % Allowed : 1.28 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.18), residues: 2340 helix: -1.15 (0.16), residues: 1000 sheet: 1.05 (0.66), residues: 56 loop : -1.28 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 409 TYR 0.027 0.001 TYR C 328 PHE 0.033 0.001 PHE B 574 TRP 0.006 0.001 TRP B 286 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19388) covalent geometry : angle 0.71758 / 0.34 (26324) hydrogen bonds : bond 0.03062 / 2.00 ( 484) hydrogen bonds : angle 4.14530 / 2.83 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 458 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7663 (ttp80) REVERT: A 99 MET cc_start: 0.8737 (mpp) cc_final: 0.8300 (mpp) REVERT: A 250 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8665 (mm-30) REVERT: A 260 MET cc_start: 0.9168 (mmp) cc_final: 0.8838 (mmp) REVERT: A 303 GLU cc_start: 0.8893 (pt0) cc_final: 0.8574 (pp20) REVERT: A 403 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7233 (tp30) REVERT: A 493 PHE cc_start: 0.8616 (t80) cc_final: 0.8325 (t80) REVERT: A 494 CYS cc_start: 0.9345 (m) cc_final: 0.9079 (m) REVERT: A 497 MET cc_start: 0.8839 (ttt) cc_final: 0.7828 (tmm) REVERT: A 501 ILE cc_start: 0.9558 (pt) cc_final: 0.8639 (pt) REVERT: A 509 HIS cc_start: 0.8646 (t70) cc_final: 0.8294 (t-170) REVERT: A 572 ASN cc_start: 0.8003 (m110) cc_final: 0.7666 (m110) REVERT: B 99 MET cc_start: 0.8587 (mpp) cc_final: 0.8100 (mpp) REVERT: B 245 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9122 (mmmt) REVERT: B 260 MET cc_start: 0.9181 (mmp) cc_final: 0.8603 (mmm) REVERT: B 403 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7244 (tp30) REVERT: B 493 PHE cc_start: 0.8590 (t80) cc_final: 0.8321 (t80) REVERT: B 497 MET cc_start: 0.8797 (ttt) cc_final: 0.7783 (tmm) REVERT: B 501 ILE cc_start: 0.9597 (pt) cc_final: 0.8503 (pt) REVERT: B 509 HIS cc_start: 0.8618 (t70) cc_final: 0.8268 (t-170) REVERT: B 603 MET cc_start: 0.8824 (tmm) cc_final: 0.8260 (tmm) REVERT: D 99 MET cc_start: 0.8697 (mpp) cc_final: 0.8342 (mpp) REVERT: D 260 MET cc_start: 0.9151 (mmp) cc_final: 0.8468 (mmm) REVERT: D 493 PHE cc_start: 0.8320 (t80) cc_final: 0.8067 (t80) REVERT: D 497 MET cc_start: 0.8807 (ttt) cc_final: 0.7905 (tmm) REVERT: D 501 ILE cc_start: 0.9584 (pt) cc_final: 0.8612 (pt) REVERT: D 509 HIS cc_start: 0.8581 (t70) cc_final: 0.8205 (t-170) REVERT: D 572 ASN cc_start: 0.8340 (m110) cc_final: 0.7771 (m110) REVERT: C 38 MET cc_start: 0.8811 (pmm) cc_final: 0.8525 (pmm) REVERT: C 59 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7638 (ttp80) REVERT: C 99 MET cc_start: 0.8656 (mpp) cc_final: 0.8320 (mpp) REVERT: C 250 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8659 (mm-30) REVERT: C 260 MET cc_start: 0.9112 (mmp) cc_final: 0.8255 (mmm) REVERT: C 261 GLN cc_start: 0.8884 (mp10) cc_final: 0.8416 (mp10) REVERT: C 403 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7152 (tp30) REVERT: C 442 MET cc_start: 0.8522 (tmm) cc_final: 0.8275 (tmm) REVERT: C 493 PHE cc_start: 0.8624 (t80) cc_final: 0.8308 (t80) REVERT: C 497 MET cc_start: 0.8768 (ttt) cc_final: 0.7765 (tmm) REVERT: C 501 ILE cc_start: 0.9582 (pt) cc_final: 0.8457 (pt) REVERT: C 509 HIS cc_start: 0.8624 (t70) cc_final: 0.8218 (t-170) outliers start: 3 outliers final: 0 residues processed: 461 average time/residue: 0.1306 time to fit residues: 95.9876 Evaluate side-chains 347 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 0.0010 chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 231 optimal weight: 0.3980 chunk 155 optimal weight: 10.0000 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN B 74 GLN C 74 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.078885 restraints weight = 54679.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081371 restraints weight = 36522.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083197 restraints weight = 26582.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084534 restraints weight = 20684.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085607 restraints weight = 16961.320| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19388 Z= 0.113 Angle : 0.724 9.076 26324 Z= 0.339 Chirality : 0.044 0.152 2984 Planarity : 0.004 0.049 3316 Dihedral : 6.127 49.528 2612 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.15 % Allowed : 0.54 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.18), residues: 2340 helix: -1.23 (0.16), residues: 1024 sheet: 1.01 (0.65), residues: 56 loop : -1.28 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.026 0.001 TYR C 328 PHE 0.028 0.001 PHE B 574 TRP 0.011 0.001 TRP B 613 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (19388) covalent geometry : angle 0.72360 / 0.34 (26324) hydrogen bonds : bond 0.03029 / 1.99 ( 484) hydrogen bonds : angle 4.09277 / 2.79 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 458 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7692 (ttp80) REVERT: A 99 MET cc_start: 0.8724 (mpp) cc_final: 0.8329 (mpp) REVERT: A 215 MET cc_start: 0.8528 (ppp) cc_final: 0.7828 (tmm) REVERT: A 250 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 260 MET cc_start: 0.9161 (mmp) cc_final: 0.8842 (mmp) REVERT: A 403 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7166 (tp30) REVERT: A 447 MET cc_start: 0.6681 (ttt) cc_final: 0.6354 (tpp) REVERT: A 493 PHE cc_start: 0.8591 (t80) cc_final: 0.8336 (t80) REVERT: A 494 CYS cc_start: 0.9367 (m) cc_final: 0.9117 (m) REVERT: A 497 MET cc_start: 0.8832 (ttt) cc_final: 0.7792 (tmm) REVERT: A 501 ILE cc_start: 0.9550 (pt) cc_final: 0.8595 (pt) REVERT: A 509 HIS cc_start: 0.8581 (t70) cc_final: 0.8261 (t-170) REVERT: A 632 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8441 (tmm-80) REVERT: B 99 MET cc_start: 0.8561 (mpp) cc_final: 0.8070 (mpp) REVERT: B 245 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9104 (mmmt) REVERT: B 294 GLU cc_start: 0.8983 (pt0) cc_final: 0.8309 (pt0) REVERT: B 403 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7264 (tp30) REVERT: B 447 MET cc_start: 0.8334 (tpt) cc_final: 0.7801 (tpp) REVERT: B 493 PHE cc_start: 0.8585 (t80) cc_final: 0.8262 (t80) REVERT: B 497 MET cc_start: 0.8856 (ttt) cc_final: 0.7818 (tmm) REVERT: B 501 ILE cc_start: 0.9568 (pt) cc_final: 0.8543 (pt) REVERT: B 509 HIS cc_start: 0.8598 (t70) cc_final: 0.8258 (t-170) REVERT: B 572 ASN cc_start: 0.8006 (m110) cc_final: 0.7722 (m110) REVERT: B 603 MET cc_start: 0.8774 (tmm) cc_final: 0.8275 (tmm) REVERT: D 99 MET cc_start: 0.8678 (mpp) cc_final: 0.8328 (mpp) REVERT: D 127 ASN cc_start: 0.8969 (p0) cc_final: 0.8740 (p0) REVERT: D 246 LEU cc_start: 0.9631 (mt) cc_final: 0.9422 (mt) REVERT: D 250 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8811 (mm-30) REVERT: D 252 ASN cc_start: 0.9259 (t0) cc_final: 0.8857 (t0) REVERT: D 260 MET cc_start: 0.9112 (mmp) cc_final: 0.8446 (mmm) REVERT: D 447 MET cc_start: 0.7574 (tpt) cc_final: 0.7212 (tpp) REVERT: D 481 MET cc_start: 0.8644 (ttt) cc_final: 0.8415 (ttt) REVERT: D 485 MET cc_start: 0.8334 (tpp) cc_final: 0.8049 (ttm) REVERT: D 497 MET cc_start: 0.8839 (ttt) cc_final: 0.7901 (tmm) REVERT: D 501 ILE cc_start: 0.9583 (pt) cc_final: 0.8635 (pt) REVERT: D 509 HIS cc_start: 0.8562 (t70) cc_final: 0.8205 (t-170) REVERT: D 572 ASN cc_start: 0.8167 (m110) cc_final: 0.7764 (m110) REVERT: C 59 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7642 (ttp80) REVERT: C 99 MET cc_start: 0.8628 (mpp) cc_final: 0.8303 (mpp) REVERT: C 127 ASN cc_start: 0.8910 (p0) cc_final: 0.8682 (p0) REVERT: C 215 MET cc_start: 0.8538 (ppp) cc_final: 0.7884 (tmm) REVERT: C 250 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 260 MET cc_start: 0.9143 (mmp) cc_final: 0.8254 (mmm) REVERT: C 261 GLN cc_start: 0.8849 (mp10) cc_final: 0.8408 (mp10) REVERT: C 403 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7150 (tp30) REVERT: C 497 MET cc_start: 0.8747 (ttt) cc_final: 0.7773 (tmm) REVERT: C 501 ILE cc_start: 0.9560 (pt) cc_final: 0.8515 (pt) REVERT: C 509 HIS cc_start: 0.8580 (t70) cc_final: 0.8204 (t-170) outliers start: 3 outliers final: 0 residues processed: 461 average time/residue: 0.1286 time to fit residues: 94.7423 Evaluate side-chains 360 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 81 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 310 GLN D 74 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.099236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079769 restraints weight = 54362.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082313 restraints weight = 35844.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084180 restraints weight = 25957.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085603 restraints weight = 20129.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086674 restraints weight = 16403.231| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19388 Z= 0.108 Angle : 0.723 8.998 26324 Z= 0.336 Chirality : 0.044 0.134 2984 Planarity : 0.003 0.048 3316 Dihedral : 5.910 48.027 2612 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.18), residues: 2340 helix: -1.21 (0.16), residues: 1020 sheet: 1.11 (0.66), residues: 56 loop : -1.24 (0.19), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.025 0.001 TYR C 328 PHE 0.031 0.001 PHE D 493 TRP 0.006 0.001 TRP B 286 HIS 0.003 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (19388) covalent geometry : angle 0.72341 / 0.34 (26324) hydrogen bonds : bond 0.02958 / 1.95 ( 484) hydrogen bonds : angle 3.99567 / 2.72 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 469 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7697 (ttp80) REVERT: A 99 MET cc_start: 0.8724 (mpp) cc_final: 0.8326 (mpp) REVERT: A 215 MET cc_start: 0.8508 (ppp) cc_final: 0.7821 (tmm) REVERT: A 246 LEU cc_start: 0.9651 (mt) cc_final: 0.9424 (mt) REVERT: A 250 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8728 (mm-30) REVERT: A 252 ASN cc_start: 0.9078 (t0) cc_final: 0.8659 (t0) REVERT: A 260 MET cc_start: 0.9137 (mmp) cc_final: 0.8449 (mmm) REVERT: A 403 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7153 (tp30) REVERT: A 447 MET cc_start: 0.6602 (ttt) cc_final: 0.6349 (tpp) REVERT: A 493 PHE cc_start: 0.8584 (t80) cc_final: 0.8347 (t80) REVERT: A 494 CYS cc_start: 0.9365 (m) cc_final: 0.9121 (m) REVERT: A 497 MET cc_start: 0.8744 (ttt) cc_final: 0.7758 (tmm) REVERT: A 501 ILE cc_start: 0.9526 (pt) cc_final: 0.8639 (pt) REVERT: A 509 HIS cc_start: 0.8545 (t70) cc_final: 0.8252 (t-170) REVERT: B 99 MET cc_start: 0.8551 (mpp) cc_final: 0.8115 (mpp) REVERT: B 245 LYS cc_start: 0.9434 (mmmt) cc_final: 0.9114 (mmmm) REVERT: B 250 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8990 (mm-30) REVERT: B 260 MET cc_start: 0.9062 (mmp) cc_final: 0.8660 (mmp) REVERT: B 279 ASP cc_start: 0.8826 (t0) cc_final: 0.8593 (t0) REVERT: B 403 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7279 (tp30) REVERT: B 447 MET cc_start: 0.8113 (tpt) cc_final: 0.7749 (tpt) REVERT: B 493 PHE cc_start: 0.8584 (t80) cc_final: 0.8299 (t80) REVERT: B 497 MET cc_start: 0.8765 (ttt) cc_final: 0.7949 (tmm) REVERT: B 501 ILE cc_start: 0.9542 (pt) cc_final: 0.8884 (pt) REVERT: B 509 HIS cc_start: 0.8572 (t70) cc_final: 0.8299 (t-170) REVERT: B 522 GLU cc_start: 0.8201 (tp30) cc_final: 0.7758 (tp30) REVERT: B 572 ASN cc_start: 0.8125 (m110) cc_final: 0.7823 (m110) REVERT: B 603 MET cc_start: 0.8771 (tmm) cc_final: 0.8276 (tmm) REVERT: D 80 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8807 (mp0) REVERT: D 99 MET cc_start: 0.8656 (mpp) cc_final: 0.8308 (mpp) REVERT: D 127 ASN cc_start: 0.8910 (p0) cc_final: 0.8666 (p0) REVERT: D 215 MET cc_start: 0.8520 (ppp) cc_final: 0.7831 (tmm) REVERT: D 246 LEU cc_start: 0.9644 (mt) cc_final: 0.9372 (mt) REVERT: D 250 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8705 (mm-30) REVERT: D 252 ASN cc_start: 0.9079 (t0) cc_final: 0.8690 (t0) REVERT: D 260 MET cc_start: 0.9130 (mmp) cc_final: 0.8416 (mmm) REVERT: D 485 MET cc_start: 0.8227 (tpp) cc_final: 0.7945 (ttm) REVERT: D 497 MET cc_start: 0.8768 (ttt) cc_final: 0.8197 (tmm) REVERT: D 501 ILE cc_start: 0.9572 (pt) cc_final: 0.8868 (pt) REVERT: D 509 HIS cc_start: 0.8516 (t70) cc_final: 0.8209 (t-170) REVERT: D 572 ASN cc_start: 0.8133 (m110) cc_final: 0.7791 (m110) REVERT: C 38 MET cc_start: 0.8872 (pmm) cc_final: 0.8643 (pmm) REVERT: C 59 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7675 (ttp80) REVERT: C 80 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8655 (mp0) REVERT: C 99 MET cc_start: 0.8637 (mpp) cc_final: 0.8310 (mpp) REVERT: C 127 ASN cc_start: 0.8913 (p0) cc_final: 0.8655 (p0) REVERT: C 215 MET cc_start: 0.8497 (ppp) cc_final: 0.7852 (tmm) REVERT: C 246 LEU cc_start: 0.9617 (mt) cc_final: 0.9367 (mt) REVERT: C 250 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8555 (mm-30) REVERT: C 260 MET cc_start: 0.9085 (mmp) cc_final: 0.8148 (mmm) REVERT: C 261 GLN cc_start: 0.8810 (mp10) cc_final: 0.8347 (mp10) REVERT: C 403 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7133 (tp30) REVERT: C 493 PHE cc_start: 0.8540 (t80) cc_final: 0.8271 (t80) REVERT: C 497 MET cc_start: 0.8706 (ttt) cc_final: 0.7619 (tmm) REVERT: C 501 ILE cc_start: 0.9548 (pt) cc_final: 0.8551 (pt) REVERT: C 509 HIS cc_start: 0.8617 (t70) cc_final: 0.8323 (t-170) REVERT: C 572 ASN cc_start: 0.8177 (m110) cc_final: 0.7812 (m110) outliers start: 4 outliers final: 0 residues processed: 472 average time/residue: 0.1298 time to fit residues: 97.7859 Evaluate side-chains 365 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 215 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.077488 restraints weight = 54373.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080132 restraints weight = 35206.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082078 restraints weight = 25158.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083482 restraints weight = 19250.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084612 restraints weight = 15586.952| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19388 Z= 0.119 Angle : 0.724 9.457 26324 Z= 0.340 Chirality : 0.044 0.151 2984 Planarity : 0.004 0.049 3316 Dihedral : 5.946 47.302 2612 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 2340 helix: -1.12 (0.16), residues: 1008 sheet: 1.04 (0.66), residues: 56 loop : -1.23 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.025 0.001 TYR C 328 PHE 0.029 0.001 PHE D 493 TRP 0.006 0.001 TRP B 613 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19388) covalent geometry : angle 0.72444 / 0.34 (26324) hydrogen bonds : bond 0.02976 / 1.96 ( 484) hydrogen bonds : angle 4.09982 / 2.80 ( 1332) =============================================================================== Job complete usr+sys time: 2981.47 seconds wall clock time: 52 minutes 28.13 seconds (3148.13 seconds total)