Starting phenix.real_space_refine on Tue Jun 17 02:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_7058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_7058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_7058.map" model { file = "/net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_7058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b5v_7058/06_2025/6b5v_7058_trim.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18933 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 10.84, per 1000 atoms: 0.57 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: 4.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.95 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: 4.65 Time building geometry restraints manager: 5.39 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 637 or resid 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.250 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP B 629 HIS 0.005 0.001 HIS B 157 PHE 0.029 0.002 PHE C 574 TYR 0.025 0.002 TYR B 278 ARG 0.025 0.003 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.22062 ( 484) hydrogen bonds : angle 7.77524 ( 1332) covalent geometry : bond 0.00769 (19388) covalent geometry : angle 1.23456 (26324) *********************** 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 : 2.097 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: 0.7159 (ttm) cc_final: 0.6956 (tmm) REVERT: A 509 HIS cc_start: 0.9078 (t70) cc_final: 0.8740 (t70) REVERT: A 603 MET cc_start: 0.8640 (tmt) cc_final: 0.8226 (tmm) REVERT: A 616 SER cc_start: 0.9293 (p) cc_final: 0.9021 (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: 0.9060 (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: 0.8584 (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: 0.7313 (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: 0.8167 (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: 0.8792 (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: 0.8235 (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: 0.8573 (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: 0.8235 (tmm) outliers start: 72 outliers final: 17 residues processed: 634 average time/residue: 0.3383 time to fit residues: 313.4461 Evaluate side-chains 453 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 433 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 84 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN B 73 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 513 GLN D 41 GLN D 73 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 513 GLN C 73 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 513 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.082910 restraints weight = 53248.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085391 restraints weight = 36402.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087311 restraints weight = 26997.811| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19388 Z= 0.196 Angle : 0.789 8.010 26324 Z= 0.402 Chirality : 0.047 0.161 2984 Planarity : 0.006 0.050 3316 Dihedral : 7.887 59.536 2612 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.15), residues: 2340 helix: -2.73 (0.14), residues: 988 sheet: 0.00 (0.60), residues: 56 loop : -2.19 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 583 HIS 0.004 0.001 HIS D 157 PHE 0.035 0.002 PHE C 574 TYR 0.021 0.002 TYR D 547 ARG 0.007 0.001 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 484) hydrogen bonds : angle 5.10385 ( 1332) covalent geometry : bond 0.00424 (19388) covalent geometry : angle 0.78923 (26324) *********************** 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 491 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 2.404 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: 0.8181 (tmm160) cc_final: 0.7956 (ttp80) REVERT: A 178 ILE cc_start: 0.9017 (pt) cc_final: 0.8782 (tp) REVERT: A 200 LEU cc_start: 0.9555 (mp) cc_final: 0.9336 (mm) REVERT: A 303 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 386 LEU cc_start: 0.9253 (tt) cc_final: 0.8627 (mt) REVERT: A 403 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7262 (tp30) REVERT: A 491 MET cc_start: 0.7001 (ttm) cc_final: 0.6737 (ttm) REVERT: A 497 MET cc_start: 0.8218 (ttt) cc_final: 0.7240 (tmm) REVERT: A 501 ILE cc_start: 0.9665 (pt) cc_final: 0.9234 (pt) REVERT: A 509 HIS cc_start: 0.8785 (t70) cc_final: 0.8271 (t70) REVERT: A 577 MET cc_start: 0.8014 (tpt) cc_final: 0.7650 (tpt) REVERT: A 603 MET cc_start: 0.8559 (ttt) cc_final: 0.8299 (tmm) REVERT: B 59 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7873 (ttp80) REVERT: B 99 MET cc_start: 0.8987 (mpp) cc_final: 0.8565 (mpp) REVERT: B 178 ILE cc_start: 0.8940 (pt) cc_final: 0.8660 (tp) REVERT: B 340 MET cc_start: 0.9190 (ttm) cc_final: 0.8845 (ttm) REVERT: B 386 LEU cc_start: 0.9321 (tt) cc_final: 0.8742 (mt) REVERT: B 403 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7449 (tp30) REVERT: B 421 LEU cc_start: 0.9237 (tt) cc_final: 0.9036 (tt) REVERT: B 438 LEU cc_start: 0.9028 (tt) cc_final: 0.8638 (mm) REVERT: B 497 MET cc_start: 0.8218 (ttt) cc_final: 0.7262 (tmm) REVERT: B 501 ILE cc_start: 0.9653 (pt) cc_final: 0.9186 (pt) REVERT: B 509 HIS cc_start: 0.8757 (t70) cc_final: 0.8281 (t70) REVERT: B 577 MET cc_start: 0.8043 (tpt) cc_final: 0.7782 (tpt) REVERT: B 603 MET cc_start: 0.8610 (ttt) cc_final: 0.8339 (tmm) REVERT: D 178 ILE cc_start: 0.8922 (pt) cc_final: 0.8645 (tp) REVERT: D 303 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 386 LEU cc_start: 0.9199 (tt) cc_final: 0.8509 (mt) REVERT: D 403 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7367 (tp30) REVERT: D 435 LEU cc_start: 0.8557 (tp) cc_final: 0.8341 (tp) REVERT: D 475 LEU cc_start: 0.9065 (tt) cc_final: 0.8830 (tt) REVERT: D 497 MET cc_start: 0.8137 (ttt) cc_final: 0.7061 (tmm) REVERT: D 501 ILE cc_start: 0.9697 (pt) cc_final: 0.9282 (pt) REVERT: D 509 HIS cc_start: 0.8716 (t70) cc_final: 0.8270 (t70) REVERT: D 577 MET cc_start: 0.8597 (tpt) cc_final: 0.8131 (tpt) REVERT: D 603 MET cc_start: 0.8671 (ttt) cc_final: 0.8337 (tmm) REVERT: C 59 ARG cc_start: 0.8077 (tmm160) cc_final: 0.7855 (ttp80) REVERT: C 126 MET cc_start: 0.8624 (ppp) cc_final: 0.8398 (ppp) REVERT: C 178 ILE cc_start: 0.8905 (pt) cc_final: 0.8618 (tp) REVERT: C 303 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 340 MET cc_start: 0.9212 (ttm) cc_final: 0.8874 (ttm) REVERT: C 386 LEU cc_start: 0.9315 (tt) cc_final: 0.8743 (mt) REVERT: C 438 LEU cc_start: 0.8986 (tt) cc_final: 0.8667 (mm) REVERT: C 475 LEU cc_start: 0.8910 (tt) cc_final: 0.8652 (tt) REVERT: C 491 MET cc_start: 0.6804 (ttm) cc_final: 0.6490 (ttm) REVERT: C 497 MET cc_start: 0.8148 (ttt) cc_final: 0.7143 (tmm) REVERT: C 501 ILE cc_start: 0.9661 (pt) cc_final: 0.9273 (pt) REVERT: C 509 HIS cc_start: 0.8769 (t70) cc_final: 0.8308 (t70) REVERT: C 577 MET cc_start: 0.8619 (tpt) cc_final: 0.8161 (tpt) REVERT: C 603 MET cc_start: 0.8576 (ttt) cc_final: 0.8324 (tmm) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.2761 time to fit residues: 211.1560 Evaluate side-chains 356 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 46 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 166 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 129 ASN A 513 GLN A 596 GLN B 41 GLN B 74 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 513 GLN B 596 GLN D 74 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 129 ASN D 513 GLN D 596 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 129 ASN C 513 GLN C 596 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086152 restraints weight = 52046.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088812 restraints weight = 35329.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090846 restraints weight = 25995.897| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3621 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= 0.107 Angle : 0.692 7.446 26324 Z= 0.335 Chirality : 0.044 0.163 2984 Planarity : 0.004 0.066 3316 Dihedral : 6.890 56.285 2612 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.16), residues: 2340 helix: -2.12 (0.14), residues: 988 sheet: 0.64 (0.64), residues: 56 loop : -1.75 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 583 HIS 0.004 0.001 HIS D 84 PHE 0.024 0.001 PHE A 408 TYR 0.020 0.001 TYR B 328 ARG 0.005 0.000 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 484) hydrogen bonds : angle 4.26591 ( 1332) covalent geometry : bond 0.00226 (19388) covalent geometry : angle 0.69152 (26324) *********************** 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 518 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 516 time to evaluate : 2.162 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: A 99 MET cc_start: 0.8797 (mpp) cc_final: 0.8436 (mpp) REVERT: A 200 LEU cc_start: 0.9547 (mp) cc_final: 0.9318 (mm) REVERT: A 340 MET cc_start: 0.9172 (ttm) cc_final: 0.8873 (ttm) REVERT: A 403 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7350 (tp30) REVERT: A 479 THR cc_start: 0.9259 (t) cc_final: 0.8643 (t) REVERT: A 485 MET cc_start: 0.8837 (ppp) cc_final: 0.7874 (ptm) REVERT: A 497 MET cc_start: 0.8214 (ttt) cc_final: 0.7301 (tmm) REVERT: A 501 ILE cc_start: 0.9655 (pt) cc_final: 0.9157 (pt) REVERT: A 509 HIS cc_start: 0.8723 (t70) cc_final: 0.8300 (t-170) REVERT: A 535 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 603 MET cc_start: 0.8608 (ttt) cc_final: 0.8373 (tmm) REVERT: A 608 MET cc_start: 0.8381 (mmm) cc_final: 0.7961 (mtm) REVERT: B 99 MET cc_start: 0.9001 (mpp) cc_final: 0.8798 (mpp) REVERT: B 178 ILE cc_start: 0.8890 (pt) cc_final: 0.8638 (tp) REVERT: B 200 LEU cc_start: 0.9547 (mp) cc_final: 0.9234 (mm) REVERT: B 340 MET cc_start: 0.9145 (ttm) cc_final: 0.8894 (ttm) REVERT: B 442 MET cc_start: 0.8108 (tmm) cc_final: 0.7792 (tmm) REVERT: B 479 THR cc_start: 0.9238 (t) cc_final: 0.8635 (t) REVERT: B 497 MET cc_start: 0.8131 (ttt) cc_final: 0.7199 (tmm) REVERT: B 501 ILE cc_start: 0.9641 (pt) cc_final: 0.9124 (pt) REVERT: B 509 HIS cc_start: 0.8676 (t70) cc_final: 0.8273 (t-170) REVERT: B 535 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 632 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8467 (tmm-80) REVERT: D 59 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7930 (ttp80) REVERT: D 178 ILE cc_start: 0.8880 (pt) cc_final: 0.8667 (tp) REVERT: D 200 LEU cc_start: 0.9537 (mp) cc_final: 0.9273 (mm) REVERT: D 309 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8026 (tm-30) REVERT: D 310 GLN cc_start: 0.7866 (tp40) cc_final: 0.7412 (tp40) REVERT: D 340 MET cc_start: 0.9175 (ttm) cc_final: 0.8893 (ttm) REVERT: D 475 LEU cc_start: 0.9047 (tt) cc_final: 0.8807 (tt) REVERT: D 485 MET cc_start: 0.8916 (ppp) cc_final: 0.8136 (ptm) REVERT: D 497 MET cc_start: 0.8094 (ttt) cc_final: 0.7141 (tmm) REVERT: D 501 ILE cc_start: 0.9659 (pt) cc_final: 0.9165 (pt) REVERT: D 509 HIS cc_start: 0.8626 (t70) cc_final: 0.8195 (t70) REVERT: D 577 MET cc_start: 0.8328 (tpt) cc_final: 0.7976 (tpt) REVERT: D 603 MET cc_start: 0.8545 (ttt) cc_final: 0.8287 (tmm) REVERT: D 608 MET cc_start: 0.8477 (mmm) cc_final: 0.8258 (tpp) REVERT: D 632 ARG cc_start: 0.8915 (ttp-170) cc_final: 0.8595 (tmm-80) REVERT: C 178 ILE cc_start: 0.8893 (pt) cc_final: 0.8682 (tp) REVERT: C 200 LEU cc_start: 0.9523 (mp) cc_final: 0.9260 (mm) REVERT: C 340 MET cc_start: 0.9217 (ttm) cc_final: 0.8904 (ttt) REVERT: C 485 MET cc_start: 0.8882 (ppp) cc_final: 0.8100 (ptm) REVERT: C 497 MET cc_start: 0.8170 (ttt) cc_final: 0.7274 (tmm) REVERT: C 501 ILE cc_start: 0.9657 (pt) cc_final: 0.9148 (pt) REVERT: C 509 HIS cc_start: 0.8681 (t70) cc_final: 0.8309 (t-170) REVERT: C 535 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7365 (tm-30) outliers start: 2 outliers final: 0 residues processed: 518 average time/residue: 0.2787 time to fit residues: 224.4448 Evaluate side-chains 375 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 213 optimal weight: 8.9990 chunk 81 optimal weight: 0.0270 chunk 226 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 513 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 118 GLN B 513 GLN D 84 HIS D 513 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 513 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083258 restraints weight = 53547.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085945 restraints weight = 35733.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087943 restraints weight = 26089.967| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4094 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= 0.115 Angle : 0.688 7.998 26324 Z= 0.330 Chirality : 0.043 0.161 2984 Planarity : 0.004 0.054 3316 Dihedral : 6.559 54.850 2612 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2340 helix: -1.93 (0.14), residues: 1036 sheet: 0.97 (0.68), residues: 56 loop : -1.81 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 286 HIS 0.004 0.001 HIS A 84 PHE 0.025 0.001 PHE C 408 TYR 0.011 0.001 TYR D 547 ARG 0.003 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 484) hydrogen bonds : angle 4.08985 ( 1332) covalent geometry : bond 0.00252 (19388) covalent geometry : angle 0.68807 (26324) *********************** 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 494 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.977 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 80 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8468 (mp0) REVERT: A 169 PHE cc_start: 0.9092 (m-80) cc_final: 0.8835 (t80) REVERT: A 303 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 403 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7382 (tp30) REVERT: A 439 THR cc_start: 0.8980 (p) cc_final: 0.8779 (p) REVERT: A 485 MET cc_start: 0.8779 (ppp) cc_final: 0.7933 (ttp) REVERT: A 497 MET cc_start: 0.8321 (ttt) cc_final: 0.7655 (tmm) REVERT: A 501 ILE cc_start: 0.9662 (pt) cc_final: 0.9074 (pt) REVERT: A 509 HIS cc_start: 0.8727 (t70) cc_final: 0.8210 (t-170) REVERT: A 535 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 608 MET cc_start: 0.8477 (mmm) cc_final: 0.8205 (tpp) REVERT: B 99 MET cc_start: 0.8931 (mpp) cc_final: 0.8490 (mpp) REVERT: B 200 LEU cc_start: 0.9546 (mp) cc_final: 0.9265 (mm) REVERT: B 294 GLU cc_start: 0.8887 (pt0) cc_final: 0.8507 (pt0) REVERT: B 430 ILE cc_start: 0.9358 (pt) cc_final: 0.9125 (mm) REVERT: B 439 THR cc_start: 0.8960 (p) cc_final: 0.8751 (p) REVERT: B 442 MET cc_start: 0.8269 (tmm) cc_final: 0.7867 (tmm) REVERT: B 485 MET cc_start: 0.8505 (ppp) cc_final: 0.7619 (ttp) REVERT: B 497 MET cc_start: 0.8274 (ttt) cc_final: 0.7400 (tmm) REVERT: B 501 ILE cc_start: 0.9678 (pt) cc_final: 0.9108 (pt) REVERT: B 509 HIS cc_start: 0.8720 (t70) cc_final: 0.8257 (t-170) REVERT: B 535 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 632 ARG cc_start: 0.8938 (ttp-170) cc_final: 0.8571 (tmm-80) REVERT: D 38 MET cc_start: 0.8703 (pmm) cc_final: 0.8445 (pmm) REVERT: D 59 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7452 (ttp80) REVERT: D 99 MET cc_start: 0.8940 (mpp) cc_final: 0.8397 (mpp) REVERT: D 178 ILE cc_start: 0.8931 (pt) cc_final: 0.8728 (tp) REVERT: D 200 LEU cc_start: 0.9549 (mp) cc_final: 0.9300 (mm) REVERT: D 303 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 475 LEU cc_start: 0.9120 (tt) cc_final: 0.8905 (tt) REVERT: D 482 ILE cc_start: 0.9120 (pt) cc_final: 0.8874 (pt) REVERT: D 485 MET cc_start: 0.8706 (ppp) cc_final: 0.7982 (ttp) REVERT: D 497 MET cc_start: 0.8296 (ttt) cc_final: 0.7659 (tmm) REVERT: D 501 ILE cc_start: 0.9673 (pt) cc_final: 0.8996 (pt) REVERT: D 509 HIS cc_start: 0.8670 (t70) cc_final: 0.8223 (t-170) REVERT: D 536 LEU cc_start: 0.8681 (tt) cc_final: 0.8420 (tt) REVERT: D 577 MET cc_start: 0.8241 (tpt) cc_final: 0.8030 (tpt) REVERT: D 603 MET cc_start: 0.8529 (ttt) cc_final: 0.8326 (tmm) REVERT: D 608 MET cc_start: 0.8519 (mmm) cc_final: 0.8108 (mtm) REVERT: C 99 MET cc_start: 0.8899 (mpp) cc_final: 0.8375 (mpp) REVERT: C 178 ILE cc_start: 0.8934 (pt) cc_final: 0.8713 (tp) REVERT: C 200 LEU cc_start: 0.9539 (mp) cc_final: 0.9295 (mm) REVERT: C 303 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 340 MET cc_start: 0.9102 (ttm) cc_final: 0.8898 (ttt) REVERT: C 403 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7269 (tp30) REVERT: C 404 ILE cc_start: 0.9295 (mm) cc_final: 0.9011 (tt) REVERT: C 447 MET cc_start: 0.6652 (ttt) cc_final: 0.6450 (tpp) REVERT: C 482 ILE cc_start: 0.9140 (pt) cc_final: 0.8901 (pt) REVERT: C 485 MET cc_start: 0.8867 (ppp) cc_final: 0.7945 (ttp) REVERT: C 497 MET cc_start: 0.8305 (ttt) cc_final: 0.7666 (tmm) REVERT: C 501 ILE cc_start: 0.9680 (pt) cc_final: 0.9053 (pt) REVERT: C 509 HIS cc_start: 0.8736 (t70) cc_final: 0.8281 (t-170) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.2855 time to fit residues: 220.0837 Evaluate side-chains 363 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 122 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 513 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 513 GLN C 513 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080130 restraints weight = 55324.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082575 restraints weight = 37031.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084472 restraints weight = 27199.190| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19388 Z= 0.136 Angle : 0.706 8.816 26324 Z= 0.342 Chirality : 0.044 0.157 2984 Planarity : 0.004 0.050 3316 Dihedral : 6.477 53.595 2612 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2340 helix: -1.46 (0.15), residues: 1012 sheet: 1.14 (0.71), residues: 56 loop : -1.63 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 593 HIS 0.005 0.001 HIS C 122 PHE 0.031 0.002 PHE B 574 TYR 0.022 0.002 TYR B 328 ARG 0.004 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 484) hydrogen bonds : angle 4.27643 ( 1332) covalent geometry : bond 0.00297 (19388) covalent geometry : angle 0.70627 (26324) *********************** 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 462 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 2.057 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: A 126 MET cc_start: 0.8735 (ttm) cc_final: 0.8476 (ttp) REVERT: A 260 MET cc_start: 0.9010 (mmp) cc_final: 0.8616 (mmm) REVERT: A 303 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 403 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 430 ILE cc_start: 0.9370 (pt) cc_final: 0.9104 (mm) REVERT: A 482 ILE cc_start: 0.9237 (pt) cc_final: 0.9030 (pt) REVERT: A 485 MET cc_start: 0.8776 (ppp) cc_final: 0.8243 (ttp) REVERT: A 493 PHE cc_start: 0.8241 (t80) cc_final: 0.7030 (t80) REVERT: A 497 MET cc_start: 0.8465 (ttt) cc_final: 0.7920 (tpp) REVERT: A 509 HIS cc_start: 0.8698 (t70) cc_final: 0.8341 (t70) REVERT: A 535 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 536 LEU cc_start: 0.8557 (tt) cc_final: 0.8348 (tt) REVERT: B 99 MET cc_start: 0.8815 (mpp) cc_final: 0.8397 (mpp) REVERT: B 245 LYS cc_start: 0.9331 (mmmt) cc_final: 0.8850 (mmmm) REVERT: B 260 MET cc_start: 0.9041 (mmp) cc_final: 0.8542 (mmm) REVERT: B 340 MET cc_start: 0.9097 (ttt) cc_final: 0.8783 (ttm) REVERT: B 442 MET cc_start: 0.8414 (tmm) cc_final: 0.7936 (tmm) REVERT: B 497 MET cc_start: 0.8431 (ttt) cc_final: 0.7636 (tmm) REVERT: B 501 ILE cc_start: 0.9674 (pt) cc_final: 0.8883 (pt) REVERT: B 509 HIS cc_start: 0.8678 (t70) cc_final: 0.8325 (t70) REVERT: B 535 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 572 ASN cc_start: 0.7941 (m110) cc_final: 0.7669 (m110) REVERT: D 59 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7560 (ttp80) REVERT: D 99 MET cc_start: 0.8849 (mpp) cc_final: 0.8305 (mpp) REVERT: D 200 LEU cc_start: 0.9533 (mp) cc_final: 0.9232 (mm) REVERT: D 260 MET cc_start: 0.8979 (mmp) cc_final: 0.8707 (mmm) REVERT: D 328 TYR cc_start: 0.8029 (t80) cc_final: 0.7724 (t80) REVERT: D 340 MET cc_start: 0.9140 (ttt) cc_final: 0.8863 (ttt) REVERT: D 430 ILE cc_start: 0.9404 (pt) cc_final: 0.9137 (mm) REVERT: D 442 MET cc_start: 0.8533 (tmm) cc_final: 0.8260 (tmm) REVERT: D 495 TRP cc_start: 0.8941 (m100) cc_final: 0.8726 (m100) REVERT: D 497 MET cc_start: 0.8606 (ttt) cc_final: 0.7844 (tmm) REVERT: D 501 ILE cc_start: 0.9675 (pt) cc_final: 0.8841 (pt) REVERT: D 509 HIS cc_start: 0.8663 (t70) cc_final: 0.8264 (t70) REVERT: D 577 MET cc_start: 0.8197 (tpt) cc_final: 0.7901 (tpt) REVERT: D 608 MET cc_start: 0.8535 (mmm) cc_final: 0.8324 (mmm) REVERT: C 99 MET cc_start: 0.8830 (mpp) cc_final: 0.8315 (mpp) REVERT: C 245 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8984 (mmmm) REVERT: C 260 MET cc_start: 0.8913 (mmp) cc_final: 0.8450 (mmm) REVERT: C 310 GLN cc_start: 0.8477 (tp40) cc_final: 0.8223 (tp40) REVERT: C 340 MET cc_start: 0.9321 (ttm) cc_final: 0.8994 (ttt) REVERT: C 403 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7326 (tp30) REVERT: C 482 ILE cc_start: 0.9259 (pt) cc_final: 0.9032 (pt) REVERT: C 485 MET cc_start: 0.8838 (ppp) cc_final: 0.8358 (ttp) REVERT: C 497 MET cc_start: 0.8456 (ttt) cc_final: 0.7643 (tmm) REVERT: C 501 ILE cc_start: 0.9671 (pt) cc_final: 0.8886 (pt) REVERT: C 509 HIS cc_start: 0.8688 (t70) cc_final: 0.8319 (t70) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3585 time to fit residues: 263.2544 Evaluate side-chains 352 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 120 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN D 74 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 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 = 0.3356 r_free = 0.3356 target = 0.098680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079919 restraints weight = 54555.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082410 restraints weight = 36608.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084223 restraints weight = 26767.757| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4948 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= 0.125 Angle : 0.701 7.756 26324 Z= 0.339 Chirality : 0.044 0.157 2984 Planarity : 0.004 0.050 3316 Dihedral : 6.365 52.508 2612 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2340 helix: -1.30 (0.15), residues: 1016 sheet: 1.00 (0.66), residues: 56 loop : -1.54 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.004 0.001 HIS B 122 PHE 0.033 0.001 PHE C 574 TYR 0.013 0.001 TYR D 328 ARG 0.004 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 484) hydrogen bonds : angle 4.19663 ( 1332) covalent geometry : bond 0.00276 (19388) covalent geometry : angle 0.70140 (26324) *********************** 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 468 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 3.150 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: A 99 MET cc_start: 0.8802 (mpp) cc_final: 0.8312 (mpp) REVERT: A 252 ASN cc_start: 0.9110 (t0) cc_final: 0.8774 (t0) REVERT: A 260 MET cc_start: 0.9026 (mmp) cc_final: 0.8607 (mmm) REVERT: A 403 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7468 (tp30) REVERT: A 430 ILE cc_start: 0.9361 (pt) cc_final: 0.9113 (mm) REVERT: A 497 MET cc_start: 0.8517 (ttt) cc_final: 0.7599 (tmm) REVERT: A 501 ILE cc_start: 0.9651 (pt) cc_final: 0.9020 (pt) REVERT: A 509 HIS cc_start: 0.8642 (t70) cc_final: 0.8264 (t70) REVERT: A 535 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 536 LEU cc_start: 0.8573 (tt) cc_final: 0.8364 (tt) REVERT: A 572 ASN cc_start: 0.8027 (m110) cc_final: 0.7625 (m110) REVERT: B 99 MET cc_start: 0.8757 (mpp) cc_final: 0.8196 (mpp) REVERT: B 245 LYS cc_start: 0.9340 (mmmt) cc_final: 0.8960 (mmmt) REVERT: B 260 MET cc_start: 0.9089 (mmp) cc_final: 0.8543 (mmm) REVERT: B 447 MET cc_start: 0.6795 (tpt) cc_final: 0.6531 (tpp) REVERT: B 497 MET cc_start: 0.8531 (ttt) cc_final: 0.7594 (tmm) REVERT: B 501 ILE cc_start: 0.9656 (pt) cc_final: 0.8811 (pt) REVERT: B 509 HIS cc_start: 0.8617 (t70) cc_final: 0.8265 (t70) REVERT: B 535 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 572 ASN cc_start: 0.7947 (m110) cc_final: 0.7501 (m110) REVERT: D 59 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7617 (ttp80) REVERT: D 99 MET cc_start: 0.8817 (mpp) cc_final: 0.8332 (mpp) REVERT: D 245 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9004 (mmmm) REVERT: D 328 TYR cc_start: 0.8018 (t80) cc_final: 0.7777 (t80) REVERT: D 430 ILE cc_start: 0.9356 (pt) cc_final: 0.9110 (mm) REVERT: D 442 MET cc_start: 0.8529 (tmm) cc_final: 0.8229 (tmm) REVERT: D 497 MET cc_start: 0.8647 (ttt) cc_final: 0.7760 (tmm) REVERT: D 501 ILE cc_start: 0.9653 (pt) cc_final: 0.8797 (pt) REVERT: D 509 HIS cc_start: 0.8661 (t70) cc_final: 0.8244 (t70) REVERT: D 572 ASN cc_start: 0.8200 (m110) cc_final: 0.7775 (m110) REVERT: D 608 MET cc_start: 0.8477 (mmm) cc_final: 0.8275 (mmm) REVERT: C 99 MET cc_start: 0.8774 (mpp) cc_final: 0.8307 (mpp) REVERT: C 245 LYS cc_start: 0.9333 (mmmt) cc_final: 0.9040 (mmmm) REVERT: C 260 MET cc_start: 0.8997 (mmp) cc_final: 0.8587 (mmm) REVERT: C 340 MET cc_start: 0.9286 (ttm) cc_final: 0.8885 (ttt) REVERT: C 403 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7301 (tp30) REVERT: C 414 ARG cc_start: 0.7122 (mtt90) cc_final: 0.6896 (mtt90) REVERT: C 430 ILE cc_start: 0.9301 (pt) cc_final: 0.9026 (mm) REVERT: C 442 MET cc_start: 0.8545 (tmm) cc_final: 0.8187 (tmm) REVERT: C 497 MET cc_start: 0.8448 (ttt) cc_final: 0.7616 (tmm) REVERT: C 501 ILE cc_start: 0.9650 (pt) cc_final: 0.8791 (pt) REVERT: C 509 HIS cc_start: 0.8653 (t70) cc_final: 0.8272 (t70) REVERT: C 572 ASN cc_start: 0.8049 (m110) cc_final: 0.7716 (m110) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.3941 time to fit residues: 293.1870 Evaluate side-chains 352 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 212 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 596 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 = 0.3271 r_free = 0.3271 target = 0.093750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.075018 restraints weight = 55326.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077521 restraints weight = 35942.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079274 restraints weight = 25757.435| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19388 Z= 0.176 Angle : 0.755 10.015 26324 Z= 0.371 Chirality : 0.046 0.154 2984 Planarity : 0.004 0.052 3316 Dihedral : 6.757 52.563 2612 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2340 helix: -1.26 (0.15), residues: 1012 sheet: 0.76 (0.64), residues: 56 loop : -1.44 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 593 HIS 0.007 0.001 HIS B 258 PHE 0.044 0.002 PHE B 574 TYR 0.024 0.002 TYR A 328 ARG 0.005 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 484) hydrogen bonds : angle 4.65946 ( 1332) covalent geometry : bond 0.00384 (19388) covalent geometry : angle 0.75463 (26324) *********************** 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 442 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 5.814 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: A 99 MET cc_start: 0.8718 (mpp) cc_final: 0.8368 (mpp) REVERT: A 260 MET cc_start: 0.9131 (mmp) cc_final: 0.8384 (mmt) REVERT: A 261 GLN cc_start: 0.8836 (mp10) cc_final: 0.8367 (mp10) REVERT: A 303 GLU cc_start: 0.8959 (pt0) cc_final: 0.8594 (pp20) REVERT: A 403 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7706 (tp30) REVERT: A 493 PHE cc_start: 0.8704 (t80) cc_final: 0.8378 (t80) REVERT: A 497 MET cc_start: 0.8769 (ttt) cc_final: 0.7750 (tmm) REVERT: A 501 ILE cc_start: 0.9680 (pt) cc_final: 0.8740 (pt) REVERT: A 509 HIS cc_start: 0.8626 (t70) cc_final: 0.8214 (t70) REVERT: B 99 MET cc_start: 0.8555 (mpp) cc_final: 0.8097 (mpp) REVERT: B 245 LYS cc_start: 0.9352 (mmmt) cc_final: 0.9085 (mmmt) REVERT: B 260 MET cc_start: 0.9149 (mmp) cc_final: 0.8687 (mmt) REVERT: B 447 MET cc_start: 0.6880 (tpt) cc_final: 0.6580 (tpp) REVERT: B 493 PHE cc_start: 0.8671 (t80) cc_final: 0.8398 (t80) REVERT: B 497 MET cc_start: 0.8661 (ttt) cc_final: 0.7953 (tmm) REVERT: B 501 ILE cc_start: 0.9670 (pt) cc_final: 0.9086 (pt) REVERT: B 509 HIS cc_start: 0.8568 (t70) cc_final: 0.8166 (t70) REVERT: D 59 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7559 (ttp80) REVERT: D 99 MET cc_start: 0.8709 (mpp) cc_final: 0.8292 (mpp) REVERT: D 245 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9114 (mmmm) REVERT: D 497 MET cc_start: 0.8818 (ttt) cc_final: 0.7781 (tmm) REVERT: D 501 ILE cc_start: 0.9652 (pt) cc_final: 0.8773 (pt) REVERT: D 509 HIS cc_start: 0.8639 (t70) cc_final: 0.8228 (t70) REVERT: D 535 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 574 PHE cc_start: 0.7917 (t80) cc_final: 0.7686 (t80) REVERT: C 99 MET cc_start: 0.8665 (mpp) cc_final: 0.8247 (mpp) REVERT: C 245 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9091 (mmmm) REVERT: C 260 MET cc_start: 0.9067 (mmp) cc_final: 0.8334 (mmt) REVERT: C 261 GLN cc_start: 0.8792 (mp10) cc_final: 0.8348 (mp10) REVERT: C 340 MET cc_start: 0.9321 (ttm) cc_final: 0.9092 (ttt) REVERT: C 403 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7263 (tp30) REVERT: C 442 MET cc_start: 0.8629 (tmm) cc_final: 0.8255 (tmm) REVERT: C 493 PHE cc_start: 0.8610 (t80) cc_final: 0.8333 (t80) REVERT: C 497 MET cc_start: 0.8706 (ttt) cc_final: 0.7709 (tmm) REVERT: C 501 ILE cc_start: 0.9687 (pt) cc_final: 0.8804 (pt) REVERT: C 509 HIS cc_start: 0.8604 (t70) cc_final: 0.8200 (t70) REVERT: C 572 ASN cc_start: 0.8126 (m110) cc_final: 0.7653 (m110) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.4274 time to fit residues: 303.3497 Evaluate side-chains 335 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 189 optimal weight: 0.4980 chunk 174 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 104 optimal weight: 0.0170 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.076430 restraints weight = 54690.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078993 restraints weight = 35412.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080880 restraints weight = 25449.926| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5560 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= 0.123 Angle : 0.725 8.485 26324 Z= 0.346 Chirality : 0.045 0.152 2984 Planarity : 0.004 0.048 3316 Dihedral : 6.473 51.948 2612 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2340 helix: -1.02 (0.16), residues: 976 sheet: 0.68 (0.62), residues: 56 loop : -1.36 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.005 0.001 HIS D 84 PHE 0.039 0.001 PHE C 574 TYR 0.027 0.001 TYR D 328 ARG 0.004 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 484) hydrogen bonds : angle 4.33726 ( 1332) covalent geometry : bond 0.00274 (19388) covalent geometry : angle 0.72538 (26324) *********************** 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: 2 poor density : 459 time to evaluate : 3.019 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 99 MET cc_start: 0.8728 (mpp) cc_final: 0.8293 (mpp) REVERT: A 127 ASN cc_start: 0.9213 (p0) cc_final: 0.8931 (p0) REVERT: A 252 ASN cc_start: 0.9300 (t0) cc_final: 0.8873 (t0) REVERT: A 260 MET cc_start: 0.9096 (mmp) cc_final: 0.8538 (mmm) REVERT: A 303 GLU cc_start: 0.8910 (pt0) cc_final: 0.8548 (pp20) REVERT: A 403 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7358 (tp30) REVERT: A 442 MET cc_start: 0.6993 (tmm) cc_final: 0.6661 (tpp) REVERT: A 447 MET cc_start: 0.6687 (ttt) cc_final: 0.6415 (tpp) REVERT: A 493 PHE cc_start: 0.8680 (t80) cc_final: 0.8374 (t80) REVERT: A 497 MET cc_start: 0.8726 (ttt) cc_final: 0.7741 (tmm) REVERT: A 501 ILE cc_start: 0.9627 (pt) cc_final: 0.8648 (pt) REVERT: A 509 HIS cc_start: 0.8577 (t70) cc_final: 0.8215 (t-170) REVERT: A 572 ASN cc_start: 0.8103 (m110) cc_final: 0.7697 (m110) REVERT: B 97 LEU cc_start: 0.8427 (pt) cc_final: 0.8169 (pt) REVERT: B 99 MET cc_start: 0.8547 (mpp) cc_final: 0.8133 (mpp) REVERT: B 213 CYS cc_start: 0.8939 (t) cc_final: 0.8707 (t) REVERT: B 245 LYS cc_start: 0.9352 (mmmt) cc_final: 0.9020 (mmmt) REVERT: B 260 MET cc_start: 0.9133 (mmp) cc_final: 0.8521 (mmm) REVERT: B 442 MET cc_start: 0.8477 (tmm) cc_final: 0.8252 (tmm) REVERT: B 493 PHE cc_start: 0.8616 (t80) cc_final: 0.8307 (t80) REVERT: B 494 CYS cc_start: 0.9414 (m) cc_final: 0.9175 (m) REVERT: B 497 MET cc_start: 0.8791 (ttt) cc_final: 0.7829 (tmm) REVERT: B 501 ILE cc_start: 0.9626 (pt) cc_final: 0.8628 (pt) REVERT: B 509 HIS cc_start: 0.8562 (t70) cc_final: 0.8241 (t-170) REVERT: D 59 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7598 (ttp80) REVERT: D 99 MET cc_start: 0.8734 (mpp) cc_final: 0.8341 (mpp) REVERT: D 245 LYS cc_start: 0.9390 (mmmt) cc_final: 0.9104 (mmmm) REVERT: D 260 MET cc_start: 0.9170 (mmp) cc_final: 0.8836 (mmt) REVERT: D 294 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 442 MET cc_start: 0.8427 (tmm) cc_final: 0.8079 (tmm) REVERT: D 493 PHE cc_start: 0.8645 (t80) cc_final: 0.8373 (t80) REVERT: D 497 MET cc_start: 0.8820 (ttt) cc_final: 0.7851 (tmm) REVERT: D 501 ILE cc_start: 0.9616 (pt) cc_final: 0.8671 (pt) REVERT: D 509 HIS cc_start: 0.8530 (t70) cc_final: 0.8117 (t-170) REVERT: D 535 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7713 (tm-30) REVERT: D 572 ASN cc_start: 0.8168 (m110) cc_final: 0.7737 (m110) REVERT: D 608 MET cc_start: 0.8392 (mmm) cc_final: 0.8146 (tpp) REVERT: C 99 MET cc_start: 0.8675 (mpp) cc_final: 0.8266 (mpp) REVERT: C 245 LYS cc_start: 0.9417 (mmmt) cc_final: 0.9150 (mmmm) REVERT: C 260 MET cc_start: 0.9045 (mmp) cc_final: 0.8633 (mmt) REVERT: C 340 MET cc_start: 0.9301 (ttm) cc_final: 0.8932 (ttt) REVERT: C 403 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7253 (tp30) REVERT: C 442 MET cc_start: 0.8452 (tmm) cc_final: 0.8234 (tmm) REVERT: C 493 PHE cc_start: 0.8555 (t80) cc_final: 0.8345 (t80) REVERT: C 497 MET cc_start: 0.8783 (ttt) cc_final: 0.7829 (tmm) REVERT: C 501 ILE cc_start: 0.9631 (pt) cc_final: 0.8660 (pt) REVERT: C 509 HIS cc_start: 0.8563 (t70) cc_final: 0.8210 (t-170) REVERT: C 535 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 572 ASN cc_start: 0.8053 (m110) cc_final: 0.7763 (m110) outliers start: 2 outliers final: 0 residues processed: 461 average time/residue: 0.3370 time to fit residues: 244.4438 Evaluate side-chains 353 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 20.0000 chunk 123 optimal weight: 0.0570 chunk 32 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 159 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 596 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 = 0.3298 r_free = 0.3298 target = 0.094677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075415 restraints weight = 55980.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077986 restraints weight = 36471.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079855 restraints weight = 26100.618| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19388 Z= 0.139 Angle : 0.740 9.561 26324 Z= 0.356 Chirality : 0.046 0.216 2984 Planarity : 0.004 0.050 3316 Dihedral : 6.537 51.198 2612 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2340 helix: -1.27 (0.15), residues: 1044 sheet: 0.49 (0.62), residues: 56 loop : -1.41 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 629 HIS 0.004 0.001 HIS D 84 PHE 0.042 0.001 PHE C 574 TYR 0.022 0.001 TYR B 328 ARG 0.004 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 484) hydrogen bonds : angle 4.38900 ( 1332) covalent geometry : bond 0.00309 (19388) covalent geometry : angle 0.73983 (26324) *********************** 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 448 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 447 time to evaluate : 2.096 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 99 MET cc_start: 0.8678 (mpp) cc_final: 0.8276 (mpp) REVERT: A 260 MET cc_start: 0.9156 (mmp) cc_final: 0.8830 (mmm) REVERT: A 303 GLU cc_start: 0.8977 (pt0) cc_final: 0.8515 (pp20) REVERT: A 403 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7483 (tp30) REVERT: A 442 MET cc_start: 0.7105 (tmm) cc_final: 0.6819 (tpp) REVERT: A 494 CYS cc_start: 0.9399 (m) cc_final: 0.9192 (m) REVERT: A 497 MET cc_start: 0.8964 (ttt) cc_final: 0.7890 (tmm) REVERT: A 501 ILE cc_start: 0.9627 (pt) cc_final: 0.8677 (pt) REVERT: A 509 HIS cc_start: 0.8592 (t70) cc_final: 0.8233 (t-170) REVERT: A 535 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 97 LEU cc_start: 0.8522 (pt) cc_final: 0.8268 (pt) REVERT: B 99 MET cc_start: 0.8482 (mpp) cc_final: 0.8074 (mpp) REVERT: B 213 CYS cc_start: 0.9035 (t) cc_final: 0.8791 (t) REVERT: B 245 LYS cc_start: 0.9358 (mmmt) cc_final: 0.9018 (mmmt) REVERT: B 260 MET cc_start: 0.9219 (mmp) cc_final: 0.8698 (mmm) REVERT: B 340 MET cc_start: 0.8992 (ttt) cc_final: 0.8737 (ttm) REVERT: B 442 MET cc_start: 0.8377 (tmm) cc_final: 0.8114 (tmm) REVERT: B 493 PHE cc_start: 0.8684 (t80) cc_final: 0.8441 (t80) REVERT: B 494 CYS cc_start: 0.9411 (m) cc_final: 0.9180 (m) REVERT: B 497 MET cc_start: 0.8890 (ttt) cc_final: 0.7955 (tmm) REVERT: B 501 ILE cc_start: 0.9615 (pt) cc_final: 0.8755 (pt) REVERT: B 509 HIS cc_start: 0.8601 (t70) cc_final: 0.8248 (t-170) REVERT: B 535 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 59 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7605 (ttp80) REVERT: D 245 LYS cc_start: 0.9402 (mmmt) cc_final: 0.9121 (mmmm) REVERT: D 260 MET cc_start: 0.9321 (mmp) cc_final: 0.8633 (mmt) REVERT: D 261 GLN cc_start: 0.8668 (mp10) cc_final: 0.8247 (mp10) REVERT: D 442 MET cc_start: 0.8434 (tmm) cc_final: 0.8168 (tmm) REVERT: D 497 MET cc_start: 0.8920 (ttt) cc_final: 0.7925 (tmm) REVERT: D 501 ILE cc_start: 0.9617 (pt) cc_final: 0.8532 (pt) REVERT: D 509 HIS cc_start: 0.8594 (t70) cc_final: 0.8225 (t-170) REVERT: D 535 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 536 LEU cc_start: 0.8523 (tt) cc_final: 0.8283 (pp) REVERT: D 572 ASN cc_start: 0.8101 (m110) cc_final: 0.7429 (m110) REVERT: D 577 MET cc_start: 0.8783 (tpt) cc_final: 0.8455 (tpt) REVERT: C 99 MET cc_start: 0.8629 (mpp) cc_final: 0.8259 (mpp) REVERT: C 245 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9205 (mmmm) REVERT: C 260 MET cc_start: 0.9195 (mmp) cc_final: 0.8993 (mmm) REVERT: C 340 MET cc_start: 0.9296 (ttm) cc_final: 0.8871 (ttt) REVERT: C 403 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7458 (tp30) REVERT: C 494 CYS cc_start: 0.9310 (m) cc_final: 0.9089 (m) REVERT: C 497 MET cc_start: 0.8950 (ttt) cc_final: 0.7918 (tmm) REVERT: C 501 ILE cc_start: 0.9630 (pt) cc_final: 0.8551 (pt) REVERT: C 509 HIS cc_start: 0.8599 (t70) cc_final: 0.8254 (t-170) REVERT: C 535 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 577 MET cc_start: 0.8340 (tpt) cc_final: 0.7953 (tpt) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.3597 time to fit residues: 257.3003 Evaluate side-chains 357 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 221 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.077018 restraints weight = 54908.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079634 restraints weight = 35898.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081545 restraints weight = 25732.174| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19388 Z= 0.114 Angle : 0.730 9.157 26324 Z= 0.345 Chirality : 0.045 0.216 2984 Planarity : 0.004 0.046 3316 Dihedral : 6.271 50.066 2612 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.15 % Allowed : 0.05 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2340 helix: -1.21 (0.15), residues: 1056 sheet: 0.63 (0.63), residues: 56 loop : -1.44 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 629 HIS 0.003 0.001 HIS D 258 PHE 0.036 0.001 PHE C 574 TYR 0.010 0.001 TYR B 547 ARG 0.004 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 484) hydrogen bonds : angle 4.18532 ( 1332) covalent geometry : bond 0.00254 (19388) covalent geometry : angle 0.72972 (26324) ********************** 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 466 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 463 time to evaluate : 2.374 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: A 99 MET cc_start: 0.8672 (mpp) cc_final: 0.8283 (mpp) REVERT: A 250 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8767 (mm-30) REVERT: A 252 ASN cc_start: 0.9067 (t0) cc_final: 0.8831 (t0) REVERT: A 260 MET cc_start: 0.9058 (mmp) cc_final: 0.8462 (mmp) REVERT: A 303 GLU cc_start: 0.8955 (pt0) cc_final: 0.8469 (pp20) REVERT: A 403 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7375 (tp30) REVERT: A 493 PHE cc_start: 0.8770 (t80) cc_final: 0.8416 (t80) REVERT: A 494 CYS cc_start: 0.9378 (m) cc_final: 0.9141 (m) REVERT: A 497 MET cc_start: 0.8876 (ttt) cc_final: 0.7809 (tmm) REVERT: A 501 ILE cc_start: 0.9609 (pt) cc_final: 0.8686 (pt) REVERT: A 509 HIS cc_start: 0.8450 (t70) cc_final: 0.8078 (t-170) REVERT: B 97 LEU cc_start: 0.8481 (pt) cc_final: 0.8276 (pt) REVERT: B 99 MET cc_start: 0.8458 (mpp) cc_final: 0.8066 (mpp) REVERT: B 245 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9011 (mmmt) REVERT: B 260 MET cc_start: 0.9158 (mmp) cc_final: 0.8645 (mmm) REVERT: B 340 MET cc_start: 0.8970 (ttt) cc_final: 0.8673 (ttm) REVERT: B 347 CYS cc_start: 0.8938 (m) cc_final: 0.8589 (m) REVERT: B 447 MET cc_start: 0.7889 (tpt) cc_final: 0.7545 (tpp) REVERT: B 490 LEU cc_start: 0.8902 (tt) cc_final: 0.8701 (tt) REVERT: B 493 PHE cc_start: 0.8669 (t80) cc_final: 0.8352 (t80) REVERT: B 494 CYS cc_start: 0.9419 (m) cc_final: 0.9143 (m) REVERT: B 497 MET cc_start: 0.8868 (ttt) cc_final: 0.7887 (tmm) REVERT: B 501 ILE cc_start: 0.9594 (pt) cc_final: 0.8686 (pt) REVERT: B 509 HIS cc_start: 0.8547 (t70) cc_final: 0.8189 (t-170) REVERT: B 535 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 59 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7641 (ttp80) REVERT: D 99 MET cc_start: 0.8777 (mpp) cc_final: 0.8320 (mpp) REVERT: D 245 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9121 (mmmm) REVERT: D 260 MET cc_start: 0.9163 (mmp) cc_final: 0.8627 (mmm) REVERT: D 294 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8369 (mt-10) REVERT: D 493 PHE cc_start: 0.8570 (t80) cc_final: 0.8360 (t80) REVERT: D 497 MET cc_start: 0.8895 (ttt) cc_final: 0.7885 (tmm) REVERT: D 501 ILE cc_start: 0.9579 (pt) cc_final: 0.8512 (pt) REVERT: D 509 HIS cc_start: 0.8501 (t70) cc_final: 0.8094 (t70) REVERT: D 535 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 572 ASN cc_start: 0.8016 (m110) cc_final: 0.7556 (m110) REVERT: D 577 MET cc_start: 0.8585 (tpt) cc_final: 0.8222 (tpt) REVERT: C 99 MET cc_start: 0.8680 (mpp) cc_final: 0.8303 (mpp) REVERT: C 245 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9209 (mmmm) REVERT: C 260 MET cc_start: 0.9090 (mmp) cc_final: 0.8780 (mmm) REVERT: C 494 CYS cc_start: 0.9287 (m) cc_final: 0.8973 (t) REVERT: C 497 MET cc_start: 0.8958 (ttt) cc_final: 0.7952 (tmm) REVERT: C 501 ILE cc_start: 0.9598 (pt) cc_final: 0.8418 (pt) REVERT: C 509 HIS cc_start: 0.8505 (t70) cc_final: 0.8156 (t-170) REVERT: C 535 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 572 ASN cc_start: 0.7965 (m110) cc_final: 0.7585 (m110) REVERT: C 577 MET cc_start: 0.8159 (tpt) cc_final: 0.7894 (tpt) outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 0.2925 time to fit residues: 214.2592 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 : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 182 optimal weight: 30.0000 chunk 71 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078731 restraints weight = 54415.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081403 restraints weight = 35374.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083370 restraints weight = 25288.077| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19388 Z= 0.109 Angle : 0.732 9.572 26324 Z= 0.342 Chirality : 0.044 0.225 2984 Planarity : 0.004 0.046 3316 Dihedral : 6.013 47.853 2612 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 0.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2340 helix: -1.19 (0.15), residues: 1056 sheet: 0.80 (0.63), residues: 56 loop : -1.43 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 629 HIS 0.003 0.000 HIS C 157 PHE 0.032 0.001 PHE B 574 TYR 0.025 0.001 TYR D 328 ARG 0.004 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 484) hydrogen bonds : angle 3.96773 ( 1332) covalent geometry : bond 0.00239 (19388) covalent geometry : angle 0.73153 (26324) =============================================================================== Job complete usr+sys time: 6587.73 seconds wall clock time: 120 minutes 14.15 seconds (7214.15 seconds total)