Starting phenix.real_space_refine on Tue Nov 19 12:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_7058_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_7058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_7058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_7058_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b5v_7058/11_2024/6b5v_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.44, per 1000 atoms: 0.55 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: 4.97 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: 1.85 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: 4.93 Time building geometry restraints manager: 5.66 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: 0.510 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.690 Find NCS groups from input model: 0.850 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.780 ------------------------------------------------------------------------------- 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= 0.493 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 *********************** 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 : 2.084 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: 0.3399 time to fit residues: 313.9813 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 : 1.901 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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= 0.272 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 *********************** 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 : 1.983 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 386 LEU cc_start: 0.9139 (tt) cc_final: 0.8680 (mt) REVERT: A 403 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7617 (tp30) REVERT: A 435 LEU cc_start: 0.8743 (tp) cc_final: 0.8449 (tp) REVERT: A 491 MET cc_start: 0.7188 (ttm) cc_final: 0.6974 (ttm) REVERT: A 497 MET cc_start: 0.9030 (ttt) cc_final: 0.7946 (tmm) REVERT: A 501 ILE cc_start: 0.9602 (pt) cc_final: 0.9248 (pt) REVERT: A 509 HIS cc_start: 0.9111 (t70) cc_final: 0.8636 (t70) REVERT: A 578 MET cc_start: 0.9086 (ttt) cc_final: 0.8721 (tmm) REVERT: A 587 GLN cc_start: 0.9148 (tp40) cc_final: 0.8945 (tp40) REVERT: A 596 GLN cc_start: 0.9206 (mt0) cc_final: 0.8979 (mm-40) REVERT: A 603 MET cc_start: 0.8732 (ttt) cc_final: 0.8422 (tmm) REVERT: B 99 MET cc_start: 0.8763 (mpp) cc_final: 0.8464 (mpp) REVERT: B 340 MET cc_start: 0.8921 (ttm) cc_final: 0.8713 (ttm) REVERT: B 386 LEU cc_start: 0.9257 (tt) cc_final: 0.8835 (mt) REVERT: B 403 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7672 (tp30) REVERT: B 421 LEU cc_start: 0.9115 (tt) cc_final: 0.8844 (tt) REVERT: B 497 MET cc_start: 0.9038 (ttt) cc_final: 0.7991 (tmm) REVERT: B 501 ILE cc_start: 0.9591 (pt) cc_final: 0.9223 (pt) REVERT: B 509 HIS cc_start: 0.9110 (t70) cc_final: 0.8676 (t70) REVERT: B 578 MET cc_start: 0.9044 (ttt) cc_final: 0.8734 (tmm) REVERT: B 587 GLN cc_start: 0.9140 (tp40) cc_final: 0.8863 (tp40) REVERT: B 596 GLN cc_start: 0.9355 (mt0) cc_final: 0.9011 (mm-40) REVERT: B 603 MET cc_start: 0.8850 (ttt) cc_final: 0.8499 (tmm) REVERT: D 126 MET cc_start: 0.9004 (ppp) cc_final: 0.8784 (ppp) REVERT: D 252 ASN cc_start: 0.9354 (t0) cc_final: 0.9145 (t0) REVERT: D 386 LEU cc_start: 0.9014 (tt) cc_final: 0.8499 (mt) REVERT: D 403 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7612 (tp30) REVERT: D 435 LEU cc_start: 0.8728 (tp) cc_final: 0.8447 (tp) REVERT: D 438 LEU cc_start: 0.9047 (tt) cc_final: 0.8836 (pp) REVERT: D 439 THR cc_start: 0.9092 (m) cc_final: 0.8887 (p) REVERT: D 497 MET cc_start: 0.9025 (ttt) cc_final: 0.7895 (tmm) REVERT: D 501 ILE cc_start: 0.9613 (pt) cc_final: 0.9279 (pt) REVERT: D 509 HIS cc_start: 0.9155 (t70) cc_final: 0.8748 (t70) REVERT: D 577 MET cc_start: 0.8372 (tpt) cc_final: 0.8115 (tpt) REVERT: D 578 MET cc_start: 0.8993 (ttt) cc_final: 0.8775 (tmm) REVERT: D 587 GLN cc_start: 0.9080 (tp40) cc_final: 0.8862 (tp40) REVERT: D 603 MET cc_start: 0.8858 (ttt) cc_final: 0.8466 (tmm) REVERT: C 126 MET cc_start: 0.9033 (ppp) cc_final: 0.8798 (ppp) REVERT: C 260 MET cc_start: 0.9042 (mmp) cc_final: 0.8790 (mmp) REVERT: C 340 MET cc_start: 0.8917 (ttm) cc_final: 0.8713 (ttm) REVERT: C 386 LEU cc_start: 0.9254 (tt) cc_final: 0.8833 (mt) REVERT: C 421 LEU cc_start: 0.9162 (tt) cc_final: 0.8955 (tt) REVERT: C 475 LEU cc_start: 0.8576 (tt) cc_final: 0.8373 (tt) REVERT: C 491 MET cc_start: 0.6893 (ttm) cc_final: 0.6656 (ttm) REVERT: C 497 MET cc_start: 0.9026 (ttt) cc_final: 0.7925 (tmm) REVERT: C 501 ILE cc_start: 0.9595 (pt) cc_final: 0.9275 (pt) REVERT: C 509 HIS cc_start: 0.9115 (t70) cc_final: 0.8693 (t70) REVERT: C 577 MET cc_start: 0.8336 (tpt) cc_final: 0.8114 (tpt) REVERT: C 587 GLN cc_start: 0.9106 (tp40) cc_final: 0.8877 (tp40) REVERT: C 596 GLN cc_start: 0.9365 (mt0) cc_final: 0.8968 (mm-40) REVERT: C 603 MET cc_start: 0.8763 (ttt) cc_final: 0.8467 (tmm) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.2910 time to fit residues: 225.1088 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 : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.0170 chunk 65 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 209 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- 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 B 41 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 129 ASN B 513 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19388 Z= 0.153 Angle : 0.683 7.776 26324 Z= 0.335 Chirality : 0.044 0.161 2984 Planarity : 0.004 0.070 3316 Dihedral : 6.955 56.340 2612 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % 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: -2.74 (0.16), residues: 2340 helix: -2.06 (0.14), residues: 988 sheet: 0.58 (0.63), residues: 56 loop : -1.71 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 286 HIS 0.005 0.001 HIS B 84 PHE 0.024 0.001 PHE A 408 TYR 0.019 0.001 TYR B 328 ARG 0.005 0.000 ARG D 59 *********************** 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 508 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 2.127 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: A 99 MET cc_start: 0.8629 (mpp) cc_final: 0.8344 (mpp) REVERT: A 479 THR cc_start: 0.9535 (t) cc_final: 0.9243 (t) REVERT: A 485 MET cc_start: 0.8577 (ppp) cc_final: 0.8330 (ptp) REVERT: A 497 MET cc_start: 0.9091 (ttt) cc_final: 0.8088 (tmm) REVERT: A 501 ILE cc_start: 0.9546 (pt) cc_final: 0.9199 (pt) REVERT: A 509 HIS cc_start: 0.9089 (t70) cc_final: 0.8672 (t-170) REVERT: A 578 MET cc_start: 0.8909 (ttt) cc_final: 0.8530 (tmm) REVERT: A 587 GLN cc_start: 0.9110 (tp40) cc_final: 0.8829 (tp40) REVERT: A 596 GLN cc_start: 0.9185 (mt0) cc_final: 0.8947 (mm-40) REVERT: A 603 MET cc_start: 0.8741 (ttt) cc_final: 0.8466 (tmm) REVERT: A 632 ARG cc_start: 0.8847 (ttp-170) cc_final: 0.8604 (tmm-80) REVERT: A 635 ASN cc_start: 0.9301 (t0) cc_final: 0.9097 (t0) REVERT: B 126 MET cc_start: 0.8943 (ppp) cc_final: 0.8649 (ppp) REVERT: B 421 LEU cc_start: 0.9069 (tt) cc_final: 0.8867 (tt) REVERT: B 439 THR cc_start: 0.9090 (m) cc_final: 0.8808 (p) REVERT: B 442 MET cc_start: 0.7740 (tmm) cc_final: 0.7313 (tmm) REVERT: B 485 MET cc_start: 0.8781 (ppp) cc_final: 0.8552 (ptm) REVERT: B 497 MET cc_start: 0.9033 (ttt) cc_final: 0.7976 (tmm) REVERT: B 501 ILE cc_start: 0.9516 (pt) cc_final: 0.9168 (pt) REVERT: B 509 HIS cc_start: 0.9081 (t70) cc_final: 0.8694 (t-170) REVERT: B 587 GLN cc_start: 0.9099 (tp40) cc_final: 0.8867 (tp40) REVERT: B 596 GLN cc_start: 0.9362 (mt0) cc_final: 0.8968 (mm-40) REVERT: B 603 MET cc_start: 0.8726 (ttt) cc_final: 0.8400 (tmm) REVERT: B 632 ARG cc_start: 0.8821 (ttp-170) cc_final: 0.8263 (tmm-80) REVERT: D 99 MET cc_start: 0.8763 (mpp) cc_final: 0.8415 (mpp) REVERT: D 252 ASN cc_start: 0.9306 (t0) cc_final: 0.8863 (t0) REVERT: D 309 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 310 GLN cc_start: 0.8572 (tp40) cc_final: 0.8078 (tp40) REVERT: D 403 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7424 (tp30) REVERT: D 435 LEU cc_start: 0.8760 (tp) cc_final: 0.8519 (tp) REVERT: D 438 LEU cc_start: 0.9074 (tt) cc_final: 0.8844 (pp) REVERT: D 485 MET cc_start: 0.8685 (ppp) cc_final: 0.8427 (ptm) REVERT: D 497 MET cc_start: 0.9082 (ttt) cc_final: 0.8047 (tmm) REVERT: D 501 ILE cc_start: 0.9540 (pt) cc_final: 0.9193 (pt) REVERT: D 509 HIS cc_start: 0.9105 (t70) cc_final: 0.8728 (t-170) REVERT: D 535 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8036 (tm-30) REVERT: D 578 MET cc_start: 0.8918 (ttt) cc_final: 0.8694 (tmm) REVERT: D 587 GLN cc_start: 0.9090 (tp40) cc_final: 0.8820 (tp40) REVERT: D 603 MET cc_start: 0.8734 (ttt) cc_final: 0.8301 (tmm) REVERT: D 608 MET cc_start: 0.7800 (mmm) cc_final: 0.7600 (tpp) REVERT: D 635 ASN cc_start: 0.9223 (t0) cc_final: 0.9002 (t0) REVERT: C 99 MET cc_start: 0.8686 (mpp) cc_final: 0.8323 (mpp) REVERT: C 485 MET cc_start: 0.8690 (ppp) cc_final: 0.8407 (ptm) REVERT: C 497 MET cc_start: 0.9078 (ttt) cc_final: 0.8036 (tmm) REVERT: C 501 ILE cc_start: 0.9527 (pt) cc_final: 0.9171 (pt) REVERT: C 509 HIS cc_start: 0.9092 (t70) cc_final: 0.8730 (t-170) REVERT: C 587 GLN cc_start: 0.9073 (tp40) cc_final: 0.8820 (tp40) REVERT: C 596 GLN cc_start: 0.9389 (mt0) cc_final: 0.8933 (mm-40) REVERT: C 603 MET cc_start: 0.8764 (ttt) cc_final: 0.8477 (tmm) REVERT: C 635 ASN cc_start: 0.9206 (t0) cc_final: 0.8979 (t0) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.2898 time to fit residues: 228.2148 Evaluate side-chains 370 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 224 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 84 HIS A 513 GLN B 74 GLN B 84 HIS B 118 GLN B 513 GLN D 84 HIS D 513 GLN C 84 HIS C 513 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19388 Z= 0.138 Angle : 0.674 8.552 26324 Z= 0.320 Chirality : 0.043 0.163 2984 Planarity : 0.003 0.054 3316 Dihedral : 6.373 54.285 2612 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.15 % Allowed : 4.54 % Favored : 95.32 % 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: -2.86 (0.16), residues: 2340 helix: -1.91 (0.14), residues: 1048 sheet: 1.03 (0.68), residues: 56 loop : -2.02 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.003 0.000 HIS A 84 PHE 0.022 0.001 PHE D 408 TYR 0.006 0.001 TYR B 547 ARG 0.006 0.000 ARG D 59 *********************** 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 515 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 512 time to evaluate : 2.124 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: A 80 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8713 (mp0) REVERT: A 328 TYR cc_start: 0.9038 (t80) cc_final: 0.8780 (t80) REVERT: A 403 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7421 (tp30) REVERT: A 485 MET cc_start: 0.8791 (ppp) cc_final: 0.8576 (ttp) REVERT: A 497 MET cc_start: 0.9110 (ttt) cc_final: 0.8093 (tmm) REVERT: A 501 ILE cc_start: 0.9487 (pt) cc_final: 0.9123 (pt) REVERT: A 509 HIS cc_start: 0.9091 (t70) cc_final: 0.8645 (t-170) REVERT: A 572 ASN cc_start: 0.8270 (m110) cc_final: 0.8066 (m110) REVERT: A 578 MET cc_start: 0.8859 (ttt) cc_final: 0.8355 (tmm) REVERT: A 587 GLN cc_start: 0.9034 (tp40) cc_final: 0.8712 (tp40) REVERT: A 603 MET cc_start: 0.8575 (ttt) cc_final: 0.8289 (tmm) REVERT: A 635 ASN cc_start: 0.9266 (t0) cc_final: 0.9037 (t0) REVERT: B 294 GLU cc_start: 0.9082 (pt0) cc_final: 0.8859 (pt0) REVERT: B 442 MET cc_start: 0.7974 (tmm) cc_final: 0.7632 (tmm) REVERT: B 485 MET cc_start: 0.8577 (ppp) cc_final: 0.8135 (ttp) REVERT: B 493 PHE cc_start: 0.8057 (t80) cc_final: 0.7453 (t80) REVERT: B 497 MET cc_start: 0.9069 (ttt) cc_final: 0.8669 (tpp) REVERT: B 509 HIS cc_start: 0.9072 (t70) cc_final: 0.8643 (t-170) REVERT: B 587 GLN cc_start: 0.9023 (tp40) cc_final: 0.8674 (tp40) REVERT: B 596 GLN cc_start: 0.9391 (mt0) cc_final: 0.8960 (mm-40) REVERT: B 603 MET cc_start: 0.8690 (ttt) cc_final: 0.8380 (tmm) REVERT: B 632 ARG cc_start: 0.8781 (ttp-170) cc_final: 0.8298 (tmm-80) REVERT: B 635 ASN cc_start: 0.9284 (t0) cc_final: 0.9052 (t0) REVERT: D 59 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7106 (ttp80) REVERT: D 99 MET cc_start: 0.8726 (mpp) cc_final: 0.8367 (mpp) REVERT: D 252 ASN cc_start: 0.9209 (t0) cc_final: 0.8801 (t0) REVERT: D 309 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 310 GLN cc_start: 0.8542 (tp40) cc_final: 0.8080 (tp40) REVERT: D 403 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7245 (tp30) REVERT: D 438 LEU cc_start: 0.9109 (tt) cc_final: 0.8886 (pp) REVERT: D 485 MET cc_start: 0.8634 (ppp) cc_final: 0.7990 (ttp) REVERT: D 497 MET cc_start: 0.9096 (ttt) cc_final: 0.8218 (tmm) REVERT: D 501 ILE cc_start: 0.9495 (pt) cc_final: 0.9086 (pt) REVERT: D 509 HIS cc_start: 0.9092 (t70) cc_final: 0.8711 (t-170) REVERT: D 535 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 578 MET cc_start: 0.8770 (ttt) cc_final: 0.8534 (tmm) REVERT: D 587 GLN cc_start: 0.8965 (tp40) cc_final: 0.8672 (tp40) REVERT: D 603 MET cc_start: 0.8609 (ttt) cc_final: 0.8240 (tmm) REVERT: C 99 MET cc_start: 0.8660 (mpp) cc_final: 0.8346 (mpp) REVERT: C 310 GLN cc_start: 0.8777 (tp40) cc_final: 0.8432 (tp40) REVERT: C 328 TYR cc_start: 0.9028 (t80) cc_final: 0.8766 (t80) REVERT: C 403 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7393 (tp30) REVERT: C 421 LEU cc_start: 0.9226 (tt) cc_final: 0.9007 (tt) REVERT: C 485 MET cc_start: 0.8699 (ppp) cc_final: 0.8144 (ttp) REVERT: C 493 PHE cc_start: 0.7992 (t80) cc_final: 0.7315 (t80) REVERT: C 497 MET cc_start: 0.9089 (ttt) cc_final: 0.8678 (tpp) REVERT: C 509 HIS cc_start: 0.9061 (t70) cc_final: 0.8651 (t-170) REVERT: C 587 GLN cc_start: 0.8998 (tp40) cc_final: 0.8614 (tp40) REVERT: C 596 GLN cc_start: 0.9338 (mt0) cc_final: 0.8872 (mm-40) REVERT: C 603 MET cc_start: 0.8679 (ttt) cc_final: 0.8370 (tmm) REVERT: C 635 ASN cc_start: 0.9041 (t0) cc_final: 0.8772 (t0) outliers start: 3 outliers final: 0 residues processed: 514 average time/residue: 0.3051 time to fit residues: 246.1163 Evaluate side-chains 381 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 191 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.0270 chunk 201 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 84 HIS B 513 GLN D 513 GLN C 74 GLN C 258 HIS C 513 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19388 Z= 0.136 Angle : 0.677 9.243 26324 Z= 0.318 Chirality : 0.042 0.163 2984 Planarity : 0.003 0.049 3316 Dihedral : 5.961 52.282 2612 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % 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: -2.52 (0.16), residues: 2340 helix: -1.62 (0.15), residues: 1028 sheet: 1.27 (0.70), residues: 56 loop : -1.85 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.004 0.000 HIS A 122 PHE 0.026 0.001 PHE B 408 TYR 0.021 0.001 TYR B 328 ARG 0.005 0.000 ARG D 59 *********************** 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 524 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 2.259 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 250 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8456 (mm-30) REVERT: A 328 TYR cc_start: 0.9051 (t80) cc_final: 0.8695 (t80) REVERT: A 403 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7328 (tp30) REVERT: A 497 MET cc_start: 0.9127 (ttt) cc_final: 0.8077 (tmm) REVERT: A 501 ILE cc_start: 0.9445 (pt) cc_final: 0.9100 (pt) REVERT: A 509 HIS cc_start: 0.9039 (t70) cc_final: 0.8580 (t-170) REVERT: A 522 GLU cc_start: 0.8114 (tp30) cc_final: 0.7486 (tp30) REVERT: A 578 MET cc_start: 0.8803 (ttt) cc_final: 0.8169 (tmm) REVERT: A 587 GLN cc_start: 0.8979 (tp40) cc_final: 0.8572 (tp40) REVERT: A 603 MET cc_start: 0.8544 (ttt) cc_final: 0.8297 (tmm) REVERT: A 608 MET cc_start: 0.7992 (tpp) cc_final: 0.7728 (tpt) REVERT: B 252 ASN cc_start: 0.8619 (t0) cc_final: 0.8322 (t0) REVERT: B 260 MET cc_start: 0.9143 (mmp) cc_final: 0.8818 (mmm) REVERT: B 294 GLU cc_start: 0.9066 (pt0) cc_final: 0.8791 (pt0) REVERT: B 439 THR cc_start: 0.9166 (p) cc_final: 0.8906 (p) REVERT: B 442 MET cc_start: 0.7948 (tmm) cc_final: 0.7586 (tmm) REVERT: B 485 MET cc_start: 0.8723 (ppp) cc_final: 0.8488 (ttp) REVERT: B 493 PHE cc_start: 0.8071 (t80) cc_final: 0.7546 (t80) REVERT: B 497 MET cc_start: 0.9119 (ttt) cc_final: 0.8687 (tpp) REVERT: B 509 HIS cc_start: 0.9041 (t70) cc_final: 0.8627 (t-170) REVERT: B 535 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 572 ASN cc_start: 0.8184 (m110) cc_final: 0.7982 (m110) REVERT: B 587 GLN cc_start: 0.8979 (tp40) cc_final: 0.8545 (tp40) REVERT: B 596 GLN cc_start: 0.9318 (mt0) cc_final: 0.8862 (mm-40) REVERT: B 603 MET cc_start: 0.8663 (ttt) cc_final: 0.8392 (tmm) REVERT: B 632 ARG cc_start: 0.8645 (ttp-170) cc_final: 0.8339 (tmm-80) REVERT: D 59 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7184 (ttp80) REVERT: D 99 MET cc_start: 0.8700 (mpp) cc_final: 0.8356 (mpp) REVERT: D 250 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8418 (mm-30) REVERT: D 252 ASN cc_start: 0.9033 (t0) cc_final: 0.8514 (t0) REVERT: D 309 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 310 GLN cc_start: 0.8399 (tp40) cc_final: 0.7993 (tp40) REVERT: D 328 TYR cc_start: 0.8951 (t80) cc_final: 0.8696 (t80) REVERT: D 403 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7210 (tp30) REVERT: D 438 LEU cc_start: 0.9094 (tt) cc_final: 0.8870 (pp) REVERT: D 485 MET cc_start: 0.8834 (ppp) cc_final: 0.8441 (ttt) REVERT: D 493 PHE cc_start: 0.8238 (t80) cc_final: 0.7667 (t80) REVERT: D 497 MET cc_start: 0.9192 (ttt) cc_final: 0.8715 (tpp) REVERT: D 509 HIS cc_start: 0.9102 (t70) cc_final: 0.8673 (t-170) REVERT: D 522 GLU cc_start: 0.8236 (tp30) cc_final: 0.7567 (tp30) REVERT: D 535 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 578 MET cc_start: 0.8678 (ttt) cc_final: 0.8469 (tmm) REVERT: D 587 GLN cc_start: 0.8958 (tp40) cc_final: 0.8552 (tp40) REVERT: D 603 MET cc_start: 0.8602 (ttt) cc_final: 0.8265 (tmm) REVERT: D 632 ARG cc_start: 0.8759 (ttp-170) cc_final: 0.8343 (tmm-80) REVERT: C 99 MET cc_start: 0.8655 (mpp) cc_final: 0.8343 (mpp) REVERT: C 132 LEU cc_start: 0.9330 (tp) cc_final: 0.9033 (pp) REVERT: C 260 MET cc_start: 0.9089 (mmp) cc_final: 0.8884 (mmm) REVERT: C 328 TYR cc_start: 0.9037 (t80) cc_final: 0.8671 (t80) REVERT: C 403 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7394 (tp30) REVERT: C 421 LEU cc_start: 0.9186 (tt) cc_final: 0.8979 (tt) REVERT: C 442 MET cc_start: 0.7920 (tmm) cc_final: 0.7541 (tmm) REVERT: C 485 MET cc_start: 0.8844 (ppp) cc_final: 0.8550 (ttp) REVERT: C 493 PHE cc_start: 0.8050 (t80) cc_final: 0.7478 (t80) REVERT: C 497 MET cc_start: 0.9133 (ttt) cc_final: 0.8723 (tpp) REVERT: C 509 HIS cc_start: 0.9044 (t70) cc_final: 0.8630 (t-170) REVERT: C 587 GLN cc_start: 0.8975 (tp40) cc_final: 0.8548 (tp40) REVERT: C 596 GLN cc_start: 0.9379 (mt0) cc_final: 0.8869 (mm-40) REVERT: C 603 MET cc_start: 0.8562 (ttt) cc_final: 0.8310 (tmm) REVERT: C 608 MET cc_start: 0.7972 (tpp) cc_final: 0.7690 (tpt) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.2873 time to fit residues: 236.4196 Evaluate side-chains 390 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 40 GLN B 84 HIS B 118 GLN B 513 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19388 Z= 0.140 Angle : 0.673 8.159 26324 Z= 0.316 Chirality : 0.043 0.158 2984 Planarity : 0.003 0.047 3316 Dihedral : 5.776 50.792 2612 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.39 (0.16), residues: 2340 helix: -1.46 (0.15), residues: 1040 sheet: 1.21 (0.67), residues: 56 loop : -1.81 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.003 0.001 HIS A 157 PHE 0.026 0.001 PHE A 493 TYR 0.013 0.001 TYR D 328 ARG 0.007 0.000 ARG C 59 *********************** 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 509 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8510 (mpp) cc_final: 0.8185 (mpp) REVERT: A 250 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8426 (mm-30) REVERT: A 252 ASN cc_start: 0.8687 (t0) cc_final: 0.8005 (t0) REVERT: A 328 TYR cc_start: 0.9121 (t80) cc_final: 0.8726 (t80) REVERT: A 403 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7335 (tp30) REVERT: A 442 MET cc_start: 0.7969 (tmm) cc_final: 0.7669 (tmm) REVERT: A 491 MET cc_start: 0.7891 (ttm) cc_final: 0.7638 (tmm) REVERT: A 497 MET cc_start: 0.9151 (ttt) cc_final: 0.8251 (tmm) REVERT: A 501 ILE cc_start: 0.9458 (pt) cc_final: 0.9083 (pt) REVERT: A 522 GLU cc_start: 0.8174 (tp30) cc_final: 0.7527 (tp30) REVERT: A 578 MET cc_start: 0.8824 (ttt) cc_final: 0.8194 (tmm) REVERT: A 587 GLN cc_start: 0.8953 (tp40) cc_final: 0.8576 (tp40) REVERT: A 603 MET cc_start: 0.8574 (ttt) cc_final: 0.8290 (tmm) REVERT: A 608 MET cc_start: 0.7816 (tpp) cc_final: 0.7568 (tpt) REVERT: B 169 PHE cc_start: 0.8591 (m-80) cc_final: 0.7825 (m-80) REVERT: B 245 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8781 (mmmm) REVERT: B 252 ASN cc_start: 0.8621 (t0) cc_final: 0.8295 (t0) REVERT: B 294 GLU cc_start: 0.9010 (pt0) cc_final: 0.8573 (pt0) REVERT: B 442 MET cc_start: 0.7956 (tmm) cc_final: 0.7642 (tmm) REVERT: B 493 PHE cc_start: 0.8160 (t80) cc_final: 0.7647 (t80) REVERT: B 497 MET cc_start: 0.9145 (ttt) cc_final: 0.8648 (tpp) REVERT: B 535 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 587 GLN cc_start: 0.8977 (tp40) cc_final: 0.8516 (tp40) REVERT: B 596 GLN cc_start: 0.9345 (mt0) cc_final: 0.8881 (mm-40) REVERT: B 603 MET cc_start: 0.8641 (ttt) cc_final: 0.8384 (tmm) REVERT: B 632 ARG cc_start: 0.8609 (ttp-170) cc_final: 0.8252 (tmm-80) REVERT: D 59 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7241 (ttp80) REVERT: D 99 MET cc_start: 0.8689 (mpp) cc_final: 0.8350 (mpp) REVERT: D 252 ASN cc_start: 0.8992 (t0) cc_final: 0.8514 (t0) REVERT: D 260 MET cc_start: 0.9066 (mmp) cc_final: 0.8836 (mmp) REVERT: D 309 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 310 GLN cc_start: 0.8481 (tp40) cc_final: 0.8037 (tp40) REVERT: D 403 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7393 (tp30) REVERT: D 438 LEU cc_start: 0.9100 (tt) cc_final: 0.8870 (pp) REVERT: D 485 MET cc_start: 0.8817 (ppp) cc_final: 0.8593 (ttp) REVERT: D 493 PHE cc_start: 0.8273 (t80) cc_final: 0.7637 (t80) REVERT: D 497 MET cc_start: 0.9187 (ttt) cc_final: 0.8671 (tpp) REVERT: D 509 HIS cc_start: 0.9128 (t70) cc_final: 0.8682 (t-170) REVERT: D 535 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 578 MET cc_start: 0.8717 (ttt) cc_final: 0.8459 (tmm) REVERT: D 587 GLN cc_start: 0.8933 (tp40) cc_final: 0.8492 (tp40) REVERT: D 603 MET cc_start: 0.8618 (ttt) cc_final: 0.8260 (tmm) REVERT: C 99 MET cc_start: 0.8567 (mpp) cc_final: 0.8264 (mpp) REVERT: C 132 LEU cc_start: 0.9388 (tp) cc_final: 0.9082 (pp) REVERT: C 260 MET cc_start: 0.9160 (mmp) cc_final: 0.8797 (mmm) REVERT: C 310 GLN cc_start: 0.8636 (tp40) cc_final: 0.8361 (tp40) REVERT: C 328 TYR cc_start: 0.9095 (t80) cc_final: 0.8713 (t80) REVERT: C 403 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7143 (tp30) REVERT: C 421 LEU cc_start: 0.9174 (tt) cc_final: 0.8949 (tt) REVERT: C 497 MET cc_start: 0.9163 (ttt) cc_final: 0.8262 (tmm) REVERT: C 501 ILE cc_start: 0.9447 (pt) cc_final: 0.9018 (pt) REVERT: C 509 HIS cc_start: 0.9034 (t70) cc_final: 0.8827 (t70) REVERT: C 572 ASN cc_start: 0.8427 (m110) cc_final: 0.8078 (m110) REVERT: C 587 GLN cc_start: 0.8960 (tp40) cc_final: 0.8490 (tp40) REVERT: C 596 GLN cc_start: 0.9397 (mt0) cc_final: 0.8869 (mm-40) REVERT: C 603 MET cc_start: 0.8600 (ttt) cc_final: 0.8324 (tmm) REVERT: C 608 MET cc_start: 0.7799 (tpp) cc_final: 0.7571 (tpt) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.2755 time to fit residues: 220.3472 Evaluate side-chains 382 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 chunk 127 optimal weight: 0.0570 chunk 163 optimal weight: 9.9990 chunk 188 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19388 Z= 0.139 Angle : 0.683 8.614 26324 Z= 0.319 Chirality : 0.043 0.153 2984 Planarity : 0.003 0.047 3316 Dihedral : 5.626 49.248 2612 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.15), residues: 1040 sheet: 1.05 (0.65), residues: 56 loop : -1.71 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 613 HIS 0.003 0.001 HIS C 157 PHE 0.022 0.001 PHE C 493 TYR 0.013 0.001 TYR D 89 ARG 0.006 0.000 ARG C 59 *********************** 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 512 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 2.152 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: A 252 ASN cc_start: 0.8469 (t0) cc_final: 0.7884 (t0) REVERT: A 328 TYR cc_start: 0.9129 (t80) cc_final: 0.8898 (t80) REVERT: A 403 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7382 (tp30) REVERT: A 442 MET cc_start: 0.7850 (tmm) cc_final: 0.7543 (tmm) REVERT: A 491 MET cc_start: 0.8285 (ttm) cc_final: 0.7857 (tmm) REVERT: A 497 MET cc_start: 0.9155 (ttt) cc_final: 0.8164 (tmm) REVERT: A 501 ILE cc_start: 0.9442 (pt) cc_final: 0.9064 (pt) REVERT: A 509 HIS cc_start: 0.9044 (t-90) cc_final: 0.8582 (t-170) REVERT: A 522 GLU cc_start: 0.8018 (tp30) cc_final: 0.7394 (tp30) REVERT: A 535 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 572 ASN cc_start: 0.8436 (m110) cc_final: 0.8106 (m110) REVERT: A 578 MET cc_start: 0.8814 (ttt) cc_final: 0.8188 (tmm) REVERT: A 603 MET cc_start: 0.8586 (ttt) cc_final: 0.8321 (tmm) REVERT: A 608 MET cc_start: 0.7631 (tpp) cc_final: 0.7387 (tpt) REVERT: B 132 LEU cc_start: 0.9340 (tp) cc_final: 0.9016 (pp) REVERT: B 245 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8883 (mmmm) REVERT: B 252 ASN cc_start: 0.8557 (t0) cc_final: 0.8087 (t0) REVERT: B 260 MET cc_start: 0.9060 (mmp) cc_final: 0.8769 (mmm) REVERT: B 294 GLU cc_start: 0.9081 (pt0) cc_final: 0.8596 (pt0) REVERT: B 340 MET cc_start: 0.8469 (ttt) cc_final: 0.8264 (ttt) REVERT: B 421 LEU cc_start: 0.9098 (tt) cc_final: 0.8895 (tt) REVERT: B 442 MET cc_start: 0.7924 (tmm) cc_final: 0.7437 (tmm) REVERT: B 450 GLU cc_start: 0.7865 (mp0) cc_final: 0.7585 (mp0) REVERT: B 497 MET cc_start: 0.9185 (ttt) cc_final: 0.8286 (tmm) REVERT: B 501 ILE cc_start: 0.9428 (pt) cc_final: 0.9066 (pt) REVERT: B 509 HIS cc_start: 0.9034 (t-90) cc_final: 0.8600 (t70) REVERT: B 522 GLU cc_start: 0.7981 (tp30) cc_final: 0.7356 (tp30) REVERT: B 535 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 587 GLN cc_start: 0.8986 (tp40) cc_final: 0.8571 (tp40) REVERT: B 596 GLN cc_start: 0.9375 (mt0) cc_final: 0.8872 (mm-40) REVERT: B 603 MET cc_start: 0.8647 (ttt) cc_final: 0.8399 (tmm) REVERT: B 632 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8199 (tmm-80) REVERT: D 59 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7310 (ttp80) REVERT: D 80 GLU cc_start: 0.8707 (mp0) cc_final: 0.8464 (mp0) REVERT: D 99 MET cc_start: 0.8670 (mpp) cc_final: 0.8347 (mpp) REVERT: D 250 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8303 (mm-30) REVERT: D 252 ASN cc_start: 0.8844 (t0) cc_final: 0.8393 (t0) REVERT: D 260 MET cc_start: 0.9110 (mmp) cc_final: 0.8567 (mmp) REVERT: D 303 GLU cc_start: 0.8387 (pt0) cc_final: 0.7961 (pp20) REVERT: D 309 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 310 GLN cc_start: 0.8534 (tp40) cc_final: 0.8127 (tp40) REVERT: D 403 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7307 (tp30) REVERT: D 438 LEU cc_start: 0.9087 (tt) cc_final: 0.8859 (pp) REVERT: D 497 MET cc_start: 0.9198 (ttt) cc_final: 0.8303 (tmm) REVERT: D 501 ILE cc_start: 0.9434 (pt) cc_final: 0.9077 (pt) REVERT: D 509 HIS cc_start: 0.9110 (t70) cc_final: 0.8865 (t70) REVERT: D 522 GLU cc_start: 0.8218 (tp30) cc_final: 0.7586 (tp30) REVERT: D 535 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 572 ASN cc_start: 0.8414 (m110) cc_final: 0.8099 (m110) REVERT: D 578 MET cc_start: 0.8746 (ttt) cc_final: 0.8462 (tmm) REVERT: D 587 GLN cc_start: 0.8903 (tp40) cc_final: 0.8435 (tp40) REVERT: D 603 MET cc_start: 0.8598 (ttt) cc_final: 0.8278 (tmm) REVERT: C 99 MET cc_start: 0.8635 (mpp) cc_final: 0.8315 (mpp) REVERT: C 132 LEU cc_start: 0.9393 (tp) cc_final: 0.9103 (pp) REVERT: C 252 ASN cc_start: 0.8662 (t0) cc_final: 0.8021 (t0) REVERT: C 303 GLU cc_start: 0.8404 (pt0) cc_final: 0.8110 (pp20) REVERT: C 328 TYR cc_start: 0.9111 (t80) cc_final: 0.8740 (t80) REVERT: C 403 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7504 (tp30) REVERT: C 421 LEU cc_start: 0.9165 (tt) cc_final: 0.8945 (tt) REVERT: C 493 PHE cc_start: 0.8122 (t80) cc_final: 0.7293 (t80) REVERT: C 497 MET cc_start: 0.9172 (ttt) cc_final: 0.8552 (tpp) REVERT: C 509 HIS cc_start: 0.9020 (t70) cc_final: 0.8801 (t70) REVERT: C 535 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 542 ASP cc_start: 0.7365 (p0) cc_final: 0.7159 (p0) REVERT: C 572 ASN cc_start: 0.8369 (m110) cc_final: 0.7920 (m110) REVERT: C 587 GLN cc_start: 0.8912 (tp40) cc_final: 0.8603 (tp40) REVERT: C 596 GLN cc_start: 0.9416 (mt0) cc_final: 0.8818 (mm-40) REVERT: C 603 MET cc_start: 0.8575 (ttt) cc_final: 0.8325 (tmm) REVERT: C 608 MET cc_start: 0.7709 (tpp) cc_final: 0.7456 (tpt) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.2799 time to fit residues: 224.5824 Evaluate side-chains 397 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.0470 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 40 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 513 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 165 HIS C 513 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4934 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= 0.161 Angle : 0.703 9.135 26324 Z= 0.331 Chirality : 0.044 0.150 2984 Planarity : 0.003 0.047 3316 Dihedral : 5.675 48.447 2612 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -2.13 (0.17), residues: 2340 helix: -1.27 (0.15), residues: 1068 sheet: 0.96 (0.64), residues: 56 loop : -1.64 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 495 HIS 0.006 0.001 HIS B 84 PHE 0.029 0.001 PHE B 574 TYR 0.024 0.001 TYR D 328 ARG 0.007 0.000 ARG B 59 *********************** 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 485 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.928 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: A 99 MET cc_start: 0.8454 (mpp) cc_final: 0.8127 (mpp) REVERT: A 252 ASN cc_start: 0.8526 (t0) cc_final: 0.7930 (t0) REVERT: A 403 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7380 (tp30) REVERT: A 442 MET cc_start: 0.7988 (tmm) cc_final: 0.7668 (tmm) REVERT: A 491 MET cc_start: 0.8214 (ttm) cc_final: 0.7782 (tmm) REVERT: A 497 MET cc_start: 0.9212 (ttt) cc_final: 0.8269 (tmm) REVERT: A 501 ILE cc_start: 0.9408 (pt) cc_final: 0.9095 (pt) REVERT: A 509 HIS cc_start: 0.9024 (t-90) cc_final: 0.8514 (t-170) REVERT: A 535 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 578 MET cc_start: 0.8943 (ttt) cc_final: 0.8159 (tmm) REVERT: A 596 GLN cc_start: 0.9319 (mt0) cc_final: 0.8949 (mm-40) REVERT: A 603 MET cc_start: 0.8582 (ttt) cc_final: 0.8308 (tmm) REVERT: A 608 MET cc_start: 0.7659 (tpp) cc_final: 0.7369 (tpt) REVERT: B 41 GLN cc_start: 0.9199 (mp10) cc_final: 0.8981 (mp10) REVERT: B 245 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8985 (mmmm) REVERT: B 252 ASN cc_start: 0.8584 (t0) cc_final: 0.8082 (t0) REVERT: B 442 MET cc_start: 0.7930 (tmm) cc_final: 0.7653 (tmm) REVERT: B 493 PHE cc_start: 0.8509 (t80) cc_final: 0.8100 (t80) REVERT: B 497 MET cc_start: 0.9251 (ttt) cc_final: 0.8634 (ptm) REVERT: B 509 HIS cc_start: 0.8983 (t-90) cc_final: 0.8520 (t-170) REVERT: B 535 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 572 ASN cc_start: 0.8429 (m110) cc_final: 0.8013 (m110) REVERT: B 596 GLN cc_start: 0.9336 (mt0) cc_final: 0.8800 (mm-40) REVERT: B 603 MET cc_start: 0.8649 (ttt) cc_final: 0.8399 (tmm) REVERT: D 59 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7305 (ttp80) REVERT: D 99 MET cc_start: 0.8643 (mpp) cc_final: 0.8338 (mpp) REVERT: D 250 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8350 (mm-30) REVERT: D 252 ASN cc_start: 0.8879 (t0) cc_final: 0.8443 (t0) REVERT: D 309 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 310 GLN cc_start: 0.8582 (tp40) cc_final: 0.8150 (tp40) REVERT: D 403 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7430 (tp30) REVERT: D 491 MET cc_start: 0.7887 (ttm) cc_final: 0.7639 (tmm) REVERT: D 497 MET cc_start: 0.9242 (ttt) cc_final: 0.8652 (ptm) REVERT: D 509 HIS cc_start: 0.9116 (t70) cc_final: 0.8849 (t70) REVERT: D 535 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 572 ASN cc_start: 0.8420 (m110) cc_final: 0.8066 (m110) REVERT: D 578 MET cc_start: 0.8956 (ttt) cc_final: 0.8485 (tmm) REVERT: D 603 MET cc_start: 0.8622 (ttt) cc_final: 0.8282 (tmm) REVERT: C 99 MET cc_start: 0.8568 (mpp) cc_final: 0.8288 (mpp) REVERT: C 132 LEU cc_start: 0.9423 (tp) cc_final: 0.9123 (pp) REVERT: C 252 ASN cc_start: 0.8700 (t0) cc_final: 0.8036 (t0) REVERT: C 403 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7429 (tp30) REVERT: C 421 LEU cc_start: 0.9030 (tt) cc_final: 0.8809 (tt) REVERT: C 474 MET cc_start: 0.7725 (ppp) cc_final: 0.7360 (pmm) REVERT: C 493 PHE cc_start: 0.8245 (t80) cc_final: 0.7984 (t80) REVERT: C 497 MET cc_start: 0.9217 (ttt) cc_final: 0.8615 (ptm) REVERT: C 509 HIS cc_start: 0.9021 (t70) cc_final: 0.8791 (t70) REVERT: C 535 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7986 (tm-30) REVERT: C 596 GLN cc_start: 0.9377 (mt0) cc_final: 0.8787 (mm-40) REVERT: C 603 MET cc_start: 0.8651 (ttt) cc_final: 0.8412 (tmm) REVERT: C 608 MET cc_start: 0.7670 (tpp) cc_final: 0.7353 (tpt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.2897 time to fit residues: 221.6990 Evaluate side-chains 392 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 10.0000 chunk 208 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 188 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 136 optimal weight: 0.0870 overall best weight: 1.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 84 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19388 Z= 0.152 Angle : 0.706 8.252 26324 Z= 0.331 Chirality : 0.044 0.144 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.571 47.199 2612 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.04 (0.17), residues: 2340 helix: -1.25 (0.15), residues: 1052 sheet: 0.97 (0.64), residues: 56 loop : -1.52 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.007 0.001 HIS B 122 PHE 0.025 0.001 PHE B 574 TYR 0.019 0.001 TYR A 328 ARG 0.007 0.000 ARG B 59 *********************** 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 492 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 2.468 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: A 99 MET cc_start: 0.8442 (mpp) cc_final: 0.8124 (mpp) REVERT: A 126 MET cc_start: 0.9360 (ttp) cc_final: 0.9083 (ppp) REVERT: A 250 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 252 ASN cc_start: 0.8606 (t0) cc_final: 0.7944 (t0) REVERT: A 328 TYR cc_start: 0.8942 (t80) cc_final: 0.8671 (t80) REVERT: A 403 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7583 (tp30) REVERT: A 442 MET cc_start: 0.7882 (tmm) cc_final: 0.7550 (tmm) REVERT: A 491 MET cc_start: 0.8400 (ttm) cc_final: 0.8002 (tmm) REVERT: A 494 CYS cc_start: 0.9455 (m) cc_final: 0.9251 (m) REVERT: A 497 MET cc_start: 0.9253 (ttt) cc_final: 0.8426 (tmm) REVERT: A 501 ILE cc_start: 0.9414 (pt) cc_final: 0.9041 (pt) REVERT: A 535 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 578 MET cc_start: 0.8864 (ttt) cc_final: 0.8242 (tmm) REVERT: A 596 GLN cc_start: 0.9375 (mt0) cc_final: 0.8991 (mm-40) REVERT: A 603 MET cc_start: 0.8610 (ttt) cc_final: 0.8343 (tmm) REVERT: B 206 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 245 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8954 (mmmt) REVERT: B 250 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8442 (mm-30) REVERT: B 252 ASN cc_start: 0.8581 (t0) cc_final: 0.8128 (t0) REVERT: B 442 MET cc_start: 0.7893 (tmm) cc_final: 0.7629 (tmm) REVERT: B 497 MET cc_start: 0.9260 (ttt) cc_final: 0.8320 (tmm) REVERT: B 501 ILE cc_start: 0.9436 (pt) cc_final: 0.9054 (pt) REVERT: B 522 GLU cc_start: 0.7899 (tp30) cc_final: 0.7313 (tp30) REVERT: B 535 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 596 GLN cc_start: 0.9340 (mt0) cc_final: 0.8773 (mm-40) REVERT: B 603 MET cc_start: 0.8642 (ttt) cc_final: 0.8398 (tmm) REVERT: D 59 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7351 (ttp80) REVERT: D 99 MET cc_start: 0.8599 (mpp) cc_final: 0.8301 (mpp) REVERT: D 169 PHE cc_start: 0.8558 (m-80) cc_final: 0.7592 (m-80) REVERT: D 250 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 252 ASN cc_start: 0.8948 (t0) cc_final: 0.8160 (t0) REVERT: D 309 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 310 GLN cc_start: 0.8592 (tp40) cc_final: 0.8188 (tp40) REVERT: D 493 PHE cc_start: 0.8512 (t80) cc_final: 0.7600 (t80) REVERT: D 497 MET cc_start: 0.9285 (ttt) cc_final: 0.8614 (ptt) REVERT: D 509 HIS cc_start: 0.9035 (t70) cc_final: 0.8813 (t70) REVERT: D 535 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 572 ASN cc_start: 0.8387 (m110) cc_final: 0.8058 (m110) REVERT: D 578 MET cc_start: 0.8879 (ttt) cc_final: 0.8562 (tmm) REVERT: D 603 MET cc_start: 0.8637 (ttt) cc_final: 0.8295 (tmm) REVERT: C 99 MET cc_start: 0.8556 (mpp) cc_final: 0.8275 (mpp) REVERT: C 132 LEU cc_start: 0.9454 (tp) cc_final: 0.9157 (pp) REVERT: C 169 PHE cc_start: 0.8560 (m-80) cc_final: 0.7585 (m-80) REVERT: C 252 ASN cc_start: 0.8639 (t0) cc_final: 0.8029 (t0) REVERT: C 328 TYR cc_start: 0.8919 (t80) cc_final: 0.8669 (t80) REVERT: C 421 LEU cc_start: 0.9026 (tt) cc_final: 0.8799 (tt) REVERT: C 442 MET cc_start: 0.7224 (tmm) cc_final: 0.6894 (tpp) REVERT: C 509 HIS cc_start: 0.9000 (t70) cc_final: 0.8762 (t70) REVERT: C 522 GLU cc_start: 0.7873 (tp30) cc_final: 0.7288 (tp30) REVERT: C 535 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 596 GLN cc_start: 0.9388 (mt0) cc_final: 0.8800 (mm-40) REVERT: C 603 MET cc_start: 0.8670 (ttt) cc_final: 0.8447 (tmm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.2751 time to fit residues: 215.7428 Evaluate side-chains 397 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 231 optimal weight: 0.0030 chunk 212 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 19 optimal weight: 0.0370 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.4470 ------------------------------------------------------------------------------- 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 84 HIS C 84 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19388 Z= 0.156 Angle : 0.725 9.645 26324 Z= 0.339 Chirality : 0.044 0.157 2984 Planarity : 0.003 0.051 3316 Dihedral : 5.549 46.392 2612 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2340 helix: -1.36 (0.15), residues: 1064 sheet: 1.00 (0.64), residues: 56 loop : -1.48 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 629 HIS 0.003 0.001 HIS A 157 PHE 0.029 0.001 PHE B 574 TYR 0.026 0.001 TYR A 328 ARG 0.007 0.000 ARG B 59 ********************** 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 489 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8418 (mpp) cc_final: 0.8102 (mpp) REVERT: A 126 MET cc_start: 0.9359 (ttp) cc_final: 0.8917 (ppp) REVERT: A 250 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 252 ASN cc_start: 0.8381 (t0) cc_final: 0.7927 (t0) REVERT: A 303 GLU cc_start: 0.8501 (pt0) cc_final: 0.8082 (pp20) REVERT: A 328 TYR cc_start: 0.9061 (t80) cc_final: 0.8706 (t80) REVERT: A 491 MET cc_start: 0.8398 (ttm) cc_final: 0.7958 (tmm) REVERT: A 497 MET cc_start: 0.9274 (ttt) cc_final: 0.8305 (tmm) REVERT: A 501 ILE cc_start: 0.9416 (pt) cc_final: 0.9038 (pt) REVERT: A 535 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 572 ASN cc_start: 0.8369 (m110) cc_final: 0.8166 (m110) REVERT: A 577 MET cc_start: 0.8004 (tpt) cc_final: 0.7127 (mmm) REVERT: A 578 MET cc_start: 0.8859 (ttt) cc_final: 0.8207 (tmm) REVERT: A 596 GLN cc_start: 0.9392 (mt0) cc_final: 0.8981 (mm-40) REVERT: A 603 MET cc_start: 0.8658 (ttt) cc_final: 0.8419 (tmm) REVERT: B 245 LYS cc_start: 0.9254 (mmmt) cc_final: 0.9007 (mmmt) REVERT: B 250 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 252 ASN cc_start: 0.8385 (t0) cc_final: 0.8090 (t0) REVERT: B 260 MET cc_start: 0.8977 (mmp) cc_final: 0.8690 (mmm) REVERT: B 494 CYS cc_start: 0.9435 (m) cc_final: 0.9166 (m) REVERT: B 497 MET cc_start: 0.9253 (ttt) cc_final: 0.8306 (tmm) REVERT: B 501 ILE cc_start: 0.9429 (pt) cc_final: 0.9032 (pt) REVERT: B 522 GLU cc_start: 0.7882 (tp30) cc_final: 0.7306 (tp30) REVERT: B 535 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 572 ASN cc_start: 0.8414 (m110) cc_final: 0.8114 (m110) REVERT: B 596 GLN cc_start: 0.9346 (mt0) cc_final: 0.8745 (mm-40) REVERT: B 603 MET cc_start: 0.8654 (ttt) cc_final: 0.8392 (tmm) REVERT: D 59 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7357 (ttp80) REVERT: D 99 MET cc_start: 0.8565 (mpp) cc_final: 0.8280 (mpp) REVERT: D 250 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8424 (mm-30) REVERT: D 252 ASN cc_start: 0.8948 (t0) cc_final: 0.8164 (t0) REVERT: D 309 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 310 GLN cc_start: 0.8585 (tp40) cc_final: 0.8189 (tp40) REVERT: D 509 HIS cc_start: 0.9025 (t70) cc_final: 0.8805 (t70) REVERT: D 572 ASN cc_start: 0.8367 (m110) cc_final: 0.8149 (m110) REVERT: D 578 MET cc_start: 0.8923 (ttt) cc_final: 0.8501 (tmm) REVERT: D 603 MET cc_start: 0.8614 (ttt) cc_final: 0.8285 (tmm) REVERT: C 99 MET cc_start: 0.8541 (mpp) cc_final: 0.8282 (mpp) REVERT: C 132 LEU cc_start: 0.9469 (tp) cc_final: 0.9167 (pp) REVERT: C 252 ASN cc_start: 0.8586 (t0) cc_final: 0.7949 (t0) REVERT: C 328 TYR cc_start: 0.9036 (t80) cc_final: 0.8695 (t80) REVERT: C 403 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7472 (tp30) REVERT: C 421 LEU cc_start: 0.9030 (tt) cc_final: 0.8792 (tt) REVERT: C 493 PHE cc_start: 0.8528 (t80) cc_final: 0.8079 (t80) REVERT: C 497 MET cc_start: 0.9286 (ttt) cc_final: 0.8577 (ptm) REVERT: C 509 HIS cc_start: 0.8995 (t70) cc_final: 0.8734 (t70) REVERT: C 522 GLU cc_start: 0.7859 (tp30) cc_final: 0.7284 (tp30) REVERT: C 535 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 572 ASN cc_start: 0.8418 (m110) cc_final: 0.7846 (m110) REVERT: C 596 GLN cc_start: 0.9401 (mt0) cc_final: 0.8806 (mm-40) REVERT: C 603 MET cc_start: 0.8644 (ttt) cc_final: 0.8412 (tmm) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.2773 time to fit residues: 214.5234 Evaluate side-chains 391 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 189 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082322 restraints weight = 53900.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084874 restraints weight = 36665.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086775 restraints weight = 26917.634| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19388 Z= 0.159 Angle : 0.713 9.293 26324 Z= 0.335 Chirality : 0.044 0.149 2984 Planarity : 0.003 0.046 3316 Dihedral : 5.516 45.516 2612 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.25 (0.15), residues: 1064 sheet: 0.94 (0.63), residues: 56 loop : -1.44 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 629 HIS 0.004 0.001 HIS A 122 PHE 0.031 0.001 PHE B 574 TYR 0.025 0.001 TYR A 328 ARG 0.007 0.000 ARG B 59 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: