Starting phenix.real_space_refine on Sat Sep 28 17:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/09_2024/7k4c_22664_neut.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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 2 9.91 5 Br 5 7.06 5 S 160 5.16 5 C 12782 2.51 5 N 3335 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "D" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 2, '81F': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'81F': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.39, per 1000 atoms: 0.63 Number of scatterers: 19744 At special positions: 0 Unit cell: (143.45, 143.45, 126.35, 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) Br 5 34.99 Ca 2 19.99 S 160 16.00 O 3460 8.00 N 3335 7.00 C 12782 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: 5.04 Conformation dependent library (CDL) restraints added in 2.5 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 59.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.560A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.729A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.919A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.730A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 removed outlier: 4.044A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.523A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.675A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.455A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.759A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 487 removed outlier: 3.605A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.563A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.720A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.561A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.730A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.919A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.729A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 removed outlier: 4.046A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.674A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.659A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 446 removed outlier: 3.779A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.760A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 removed outlier: 3.604A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 498 " --> pdb=" O CYS B 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 566 removed outlier: 3.564A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 removed outlier: 3.720A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.561A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.587A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.729A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.918A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.730A pdb=" N ALA C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.045A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.505A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.017A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.554A pdb=" N ILE C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.675A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.707A pdb=" N ASP C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.760A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 removed outlier: 3.605A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 512 removed outlier: 3.629A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 498 " --> pdb=" O CYS C 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 566 removed outlier: 3.564A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.721A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 4.234A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.562A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.696A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.586A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.730A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.918A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.729A pdb=" N ALA D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.504A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 removed outlier: 4.045A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.506A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.018A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.555A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.522A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.674A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.660A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.708A pdb=" N ASP D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 395 " --> pdb=" O VAL D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.456A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 446 removed outlier: 3.780A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.718A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.759A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 487 removed outlier: 3.604A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 512 removed outlier: 3.628A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.758A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 566 removed outlier: 3.563A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 removed outlier: 3.721A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 4.233A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 112 removed outlier: 3.895A pdb=" N SER A 112 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 112 removed outlier: 3.897A pdb=" N SER B 112 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 270 removed outlier: 7.058A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.896A pdb=" N SER C 112 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 111 through 112 removed outlier: 3.896A pdb=" N SER D 112 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 265 through 270 removed outlier: 7.059A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2220 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: 5.85 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6705 1.37 - 1.51: 6918 1.51 - 1.66: 6309 1.66 - 1.80: 210 1.80 - 1.94: 67 Bond restraints: 20209 Sorted by residual: bond pdb=" C21 81F D 701 " pdb=" C22 81F D 701 " ideal model delta sigma weight residual 1.385 1.526 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 81F C 701 " pdb=" C22 81F C 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F B 701 " pdb=" C22 81F B 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F A 701 " pdb=" C22 81F A 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F D 702 " pdb=" C22 81F D 702 " ideal model delta sigma weight residual 1.385 1.515 -0.130 2.00e-02 2.50e+03 4.26e+01 ... (remaining 20204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 26237 2.35 - 4.69: 1010 4.69 - 7.04: 131 7.04 - 9.38: 42 9.38 - 11.73: 4 Bond angle restraints: 27424 Sorted by residual: angle pdb=" C TYR C 89 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C TYR D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C TYR A 89 " pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLN B 369 " pdb=" N GLN B 370 " pdb=" CA GLN B 370 " ideal model delta sigma weight residual 122.44 117.00 5.44 1.19e+00 7.06e-01 2.09e+01 ... (remaining 27419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 11326 16.96 - 33.91: 627 33.91 - 50.87: 139 50.87 - 67.82: 3 67.82 - 84.78: 38 Dihedral angle restraints: 12133 sinusoidal: 4985 harmonic: 7148 Sorted by residual: dihedral pdb=" CA SER A 112 " pdb=" C SER A 112 " pdb=" N GLU A 113 " pdb=" CA GLU A 113 " ideal model delta harmonic sigma weight residual 180.00 145.08 34.92 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA SER D 112 " pdb=" C SER D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual 180.00 145.14 34.86 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 12130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1993 0.051 - 0.102: 875 0.102 - 0.153: 193 0.153 - 0.204: 30 0.204 - 0.255: 11 Chirality restraints: 3102 Sorted by residual: chirality pdb=" C05 81F D 702 " pdb=" C04 81F D 702 " pdb=" C06 81F D 702 " pdb=" C08 81F D 702 " both_signs ideal model delta sigma weight residual False -2.52 -2.77 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C10 81F D 702 " pdb=" C07 81F D 702 " pdb=" C09 81F D 702 " pdb=" N01 81F D 702 " both_signs ideal model delta sigma weight residual False 2.33 2.58 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3099 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 476 " -0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO C 477 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.046 5.00e-02 4.00e+02 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5973 2.82 - 3.34: 19219 3.34 - 3.86: 30411 3.86 - 4.38: 35228 4.38 - 4.90: 56514 Nonbonded interactions: 147345 Sorted by model distance: nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 339 " pdb=" O THR B 392 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 204 " pdb=" ND2 ASN A 252 " model vdw 2.347 3.120 ... (remaining 147340 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 28 through 638 or resid 701)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 28 through 638 or resid 701)) } 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: 1.540 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: 0.920 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 43.680 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.009 0.141 20209 Z= 0.605 Angle : 1.088 11.728 27424 Z= 0.579 Chirality : 0.058 0.255 3102 Planarity : 0.007 0.084 3454 Dihedral : 12.364 84.777 7517 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.37 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.34 (0.12), residues: 2436 helix: -3.53 (0.08), residues: 1304 sheet: -3.43 (0.51), residues: 68 loop : -3.45 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 613 HIS 0.012 0.002 HIS A 522 PHE 0.029 0.003 PHE A 468 TYR 0.025 0.003 TYR D 623 ARG 0.006 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9600 (pp) cc_final: 0.9014 (pp) REVERT: A 96 MET cc_start: 0.9311 (mmm) cc_final: 0.8681 (mmm) REVERT: A 99 MET cc_start: 0.9029 (mmp) cc_final: 0.8829 (mtp) REVERT: A 122 HIS cc_start: 0.9389 (m90) cc_final: 0.8575 (m90) REVERT: A 267 GLN cc_start: 0.8339 (tt0) cc_final: 0.8101 (tp40) REVERT: A 303 GLU cc_start: 0.8739 (tt0) cc_final: 0.8200 (tp30) REVERT: A 305 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7414 (mtt180) REVERT: A 332 LEU cc_start: 0.9399 (tp) cc_final: 0.9127 (tt) REVERT: A 383 ASP cc_start: 0.9169 (t0) cc_final: 0.8737 (m-30) REVERT: A 402 VAL cc_start: 0.9265 (p) cc_final: 0.8575 (p) REVERT: A 435 MET cc_start: 0.8824 (mmt) cc_final: 0.8011 (mmm) REVERT: A 440 MET cc_start: 0.8875 (tpt) cc_final: 0.8594 (tpp) REVERT: A 442 MET cc_start: 0.9316 (tpp) cc_final: 0.8623 (tpp) REVERT: A 444 LEU cc_start: 0.9467 (mp) cc_final: 0.9172 (mt) REVERT: A 515 GLU cc_start: 0.7496 (tp30) cc_final: 0.7265 (mm-30) REVERT: A 587 HIS cc_start: 0.8857 (p-80) cc_final: 0.8201 (p-80) REVERT: A 588 GLU cc_start: 0.9061 (tt0) cc_final: 0.8781 (tt0) REVERT: A 590 ASP cc_start: 0.8562 (m-30) cc_final: 0.8077 (p0) REVERT: A 603 MET cc_start: 0.8829 (ttt) cc_final: 0.8475 (tmm) REVERT: B 92 LEU cc_start: 0.9615 (pp) cc_final: 0.9053 (pp) REVERT: B 96 MET cc_start: 0.9300 (mmm) cc_final: 0.8679 (mmm) REVERT: B 122 HIS cc_start: 0.9377 (m90) cc_final: 0.8590 (m90) REVERT: B 127 ASN cc_start: 0.9231 (t160) cc_final: 0.9028 (m-40) REVERT: B 267 GLN cc_start: 0.8383 (tt0) cc_final: 0.8114 (tp40) REVERT: B 303 GLU cc_start: 0.8772 (tt0) cc_final: 0.8136 (tm-30) REVERT: B 332 LEU cc_start: 0.9323 (tp) cc_final: 0.9036 (tt) REVERT: B 383 ASP cc_start: 0.9158 (t0) cc_final: 0.8710 (m-30) REVERT: B 386 LEU cc_start: 0.9376 (tp) cc_final: 0.9138 (mm) REVERT: B 402 VAL cc_start: 0.9293 (p) cc_final: 0.8688 (p) REVERT: B 435 MET cc_start: 0.8786 (mmt) cc_final: 0.8041 (mmt) REVERT: B 436 VAL cc_start: 0.9484 (t) cc_final: 0.9120 (p) REVERT: B 440 MET cc_start: 0.8793 (tpt) cc_final: 0.8503 (tpp) REVERT: B 441 VAL cc_start: 0.9659 (t) cc_final: 0.9411 (t) REVERT: B 442 MET cc_start: 0.9352 (tpp) cc_final: 0.8682 (tpp) REVERT: B 444 LEU cc_start: 0.9487 (mp) cc_final: 0.9182 (mt) REVERT: B 587 HIS cc_start: 0.8910 (p-80) cc_final: 0.8597 (p-80) REVERT: B 588 GLU cc_start: 0.9060 (tt0) cc_final: 0.8752 (tt0) REVERT: C 92 LEU cc_start: 0.9621 (pp) cc_final: 0.9060 (pp) REVERT: C 96 MET cc_start: 0.9303 (mmm) cc_final: 0.8721 (mmm) REVERT: C 122 HIS cc_start: 0.9387 (m90) cc_final: 0.8612 (m90) REVERT: C 127 ASN cc_start: 0.9220 (t160) cc_final: 0.8949 (m-40) REVERT: C 178 ILE cc_start: 0.9529 (mp) cc_final: 0.9255 (mp) REVERT: C 260 MET cc_start: 0.8946 (tpp) cc_final: 0.8742 (tpp) REVERT: C 279 ASP cc_start: 0.8888 (t70) cc_final: 0.8536 (t0) REVERT: C 303 GLU cc_start: 0.8771 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 305 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8324 (ttm-80) REVERT: C 323 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8489 (mmt180) REVERT: C 332 LEU cc_start: 0.9330 (tp) cc_final: 0.9030 (tt) REVERT: C 386 LEU cc_start: 0.9343 (tp) cc_final: 0.9117 (mm) REVERT: C 402 VAL cc_start: 0.9246 (p) cc_final: 0.8670 (p) REVERT: C 435 MET cc_start: 0.8890 (mmt) cc_final: 0.8296 (mmt) REVERT: C 440 MET cc_start: 0.8731 (tpt) cc_final: 0.8519 (tpp) REVERT: C 442 MET cc_start: 0.9342 (tpp) cc_final: 0.8745 (tpp) REVERT: C 485 MET cc_start: 0.8504 (ttm) cc_final: 0.7927 (ttm) REVERT: C 587 HIS cc_start: 0.8918 (p-80) cc_final: 0.8623 (p-80) REVERT: C 588 GLU cc_start: 0.9054 (tt0) cc_final: 0.8742 (tt0) REVERT: D 66 LYS cc_start: 0.9473 (tppt) cc_final: 0.9048 (tptp) REVERT: D 92 LEU cc_start: 0.9632 (pp) cc_final: 0.8956 (pp) REVERT: D 96 MET cc_start: 0.9254 (mmm) cc_final: 0.8532 (mmm) REVERT: D 99 MET cc_start: 0.8975 (mmp) cc_final: 0.8686 (mtt) REVERT: D 157 CYS cc_start: 0.9382 (m) cc_final: 0.8949 (t) REVERT: D 178 ILE cc_start: 0.9464 (mp) cc_final: 0.9206 (mp) REVERT: D 213 CYS cc_start: 0.9025 (t) cc_final: 0.8407 (t) REVERT: D 255 MET cc_start: 0.8702 (tpp) cc_final: 0.8185 (tpt) REVERT: D 274 THR cc_start: 0.8698 (m) cc_final: 0.8352 (m) REVERT: D 305 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7310 (mtt180) REVERT: D 318 SER cc_start: 0.9724 (t) cc_final: 0.9497 (p) REVERT: D 330 CYS cc_start: 0.9587 (m) cc_final: 0.9320 (m) REVERT: D 332 LEU cc_start: 0.9393 (tp) cc_final: 0.9105 (tt) REVERT: D 435 MET cc_start: 0.8879 (mmt) cc_final: 0.8201 (mmm) REVERT: D 440 MET cc_start: 0.8959 (tpt) cc_final: 0.8686 (tpp) REVERT: D 442 MET cc_start: 0.9396 (tpp) cc_final: 0.8729 (tpp) REVERT: D 444 LEU cc_start: 0.9523 (mp) cc_final: 0.9189 (mt) REVERT: D 452 VAL cc_start: 0.9460 (t) cc_final: 0.9229 (t) REVERT: D 456 PHE cc_start: 0.9186 (m-10) cc_final: 0.8718 (m-10) REVERT: D 485 MET cc_start: 0.8481 (ttm) cc_final: 0.7458 (ttm) REVERT: D 587 HIS cc_start: 0.8875 (p-80) cc_final: 0.8476 (p-80) REVERT: D 588 GLU cc_start: 0.8961 (tt0) cc_final: 0.8389 (tm-30) REVERT: D 590 ASP cc_start: 0.8673 (m-30) cc_final: 0.8359 (p0) REVERT: D 603 MET cc_start: 0.8816 (ttt) cc_final: 0.8565 (tmm) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.3169 time to fit residues: 281.7869 Evaluate side-chains 376 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 118 GLN A 197 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 118 GLN B 127 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 127 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 197 ASN D 483 GLN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20209 Z= 0.316 Angle : 0.803 10.303 27424 Z= 0.414 Chirality : 0.044 0.163 3102 Planarity : 0.005 0.067 3454 Dihedral : 10.068 89.720 2805 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.50 % Allowed : 12.83 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.52 (0.15), residues: 2436 helix: -1.70 (0.12), residues: 1392 sheet: -3.12 (0.53), residues: 68 loop : -3.15 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.005 0.001 HIS A 258 PHE 0.019 0.002 PHE D 162 TYR 0.029 0.002 TYR C 324 ARG 0.004 0.001 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 399 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9437 (pp) cc_final: 0.8910 (pp) REVERT: A 96 MET cc_start: 0.9114 (mmm) cc_final: 0.8555 (mmp) REVERT: A 122 HIS cc_start: 0.9375 (m90) cc_final: 0.8643 (m90) REVERT: A 383 ASP cc_start: 0.9088 (t0) cc_final: 0.8611 (m-30) REVERT: A 435 MET cc_start: 0.9046 (mmt) cc_final: 0.8205 (mmm) REVERT: A 440 MET cc_start: 0.8907 (tpt) cc_final: 0.8638 (tpp) REVERT: A 442 MET cc_start: 0.9026 (tpp) cc_final: 0.8738 (mmm) REVERT: A 444 LEU cc_start: 0.9577 (mp) cc_final: 0.9215 (mt) REVERT: A 515 GLU cc_start: 0.7319 (tp30) cc_final: 0.6888 (mm-30) REVERT: A 528 MET cc_start: 0.8724 (tpp) cc_final: 0.8449 (tpp) REVERT: A 577 MET cc_start: 0.8862 (tpp) cc_final: 0.8567 (tpp) REVERT: A 578 MET cc_start: 0.8211 (mmt) cc_final: 0.7940 (mmt) REVERT: A 587 HIS cc_start: 0.8875 (p-80) cc_final: 0.8334 (p-80) REVERT: A 588 GLU cc_start: 0.9115 (tt0) cc_final: 0.8912 (tt0) REVERT: A 590 ASP cc_start: 0.8686 (m-30) cc_final: 0.8159 (p0) REVERT: A 635 ASP cc_start: 0.8713 (t0) cc_final: 0.8352 (t0) REVERT: B 92 LEU cc_start: 0.9449 (pp) cc_final: 0.8933 (pp) REVERT: B 122 HIS cc_start: 0.9353 (m90) cc_final: 0.8592 (m90) REVERT: B 159 LEU cc_start: 0.9433 (tp) cc_final: 0.9102 (tt) REVERT: B 383 ASP cc_start: 0.9072 (t0) cc_final: 0.8527 (m-30) REVERT: B 435 MET cc_start: 0.9075 (mmt) cc_final: 0.8237 (mmm) REVERT: B 440 MET cc_start: 0.8879 (tpt) cc_final: 0.8599 (tpp) REVERT: B 442 MET cc_start: 0.9093 (tpp) cc_final: 0.8772 (mmm) REVERT: B 444 LEU cc_start: 0.9577 (mp) cc_final: 0.9230 (mt) REVERT: B 481 MET cc_start: 0.8639 (tpp) cc_final: 0.8357 (tpp) REVERT: B 483 GLN cc_start: 0.8456 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 528 MET cc_start: 0.8764 (tpp) cc_final: 0.8528 (tpp) REVERT: B 577 MET cc_start: 0.8828 (tpp) cc_final: 0.8619 (tpp) REVERT: B 587 HIS cc_start: 0.8889 (p-80) cc_final: 0.8344 (p-80) REVERT: B 588 GLU cc_start: 0.9087 (tt0) cc_final: 0.8881 (tt0) REVERT: B 590 ASP cc_start: 0.8713 (m-30) cc_final: 0.8117 (p0) REVERT: C 92 LEU cc_start: 0.9477 (pp) cc_final: 0.8916 (pp) REVERT: C 122 HIS cc_start: 0.9344 (m90) cc_final: 0.8629 (m90) REVERT: C 159 LEU cc_start: 0.9440 (tp) cc_final: 0.9119 (tt) REVERT: C 383 ASP cc_start: 0.9083 (t0) cc_final: 0.8559 (m-30) REVERT: C 435 MET cc_start: 0.9095 (mmt) cc_final: 0.8181 (mmt) REVERT: C 442 MET cc_start: 0.9141 (tpp) cc_final: 0.8546 (tpp) REVERT: C 481 MET cc_start: 0.8591 (tpp) cc_final: 0.8326 (tpp) REVERT: C 587 HIS cc_start: 0.8902 (p-80) cc_final: 0.8372 (p-80) REVERT: C 588 GLU cc_start: 0.9078 (tt0) cc_final: 0.8876 (tt0) REVERT: C 590 ASP cc_start: 0.8744 (m-30) cc_final: 0.8113 (p0) REVERT: D 66 LYS cc_start: 0.9511 (tppt) cc_final: 0.9047 (tptp) REVERT: D 92 LEU cc_start: 0.9482 (pp) cc_final: 0.8969 (pp) REVERT: D 96 MET cc_start: 0.9062 (mmm) cc_final: 0.8412 (mmp) REVERT: D 137 LEU cc_start: 0.9681 (mp) cc_final: 0.9469 (pp) REVERT: D 159 LEU cc_start: 0.9362 (tp) cc_final: 0.9042 (tt) REVERT: D 178 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8800 (mm) REVERT: D 318 SER cc_start: 0.9762 (t) cc_final: 0.9495 (p) REVERT: D 383 ASP cc_start: 0.9045 (t0) cc_final: 0.8500 (m-30) REVERT: D 435 MET cc_start: 0.9036 (mmt) cc_final: 0.8175 (mmt) REVERT: D 440 MET cc_start: 0.9049 (tpt) cc_final: 0.8816 (tpp) REVERT: D 442 MET cc_start: 0.9118 (tpp) cc_final: 0.8698 (tmm) REVERT: D 444 LEU cc_start: 0.9574 (mp) cc_final: 0.9246 (mt) REVERT: D 466 MET cc_start: 0.9220 (mtt) cc_final: 0.8879 (mmt) REVERT: D 485 MET cc_start: 0.8251 (ttm) cc_final: 0.7664 (ttm) REVERT: D 578 MET cc_start: 0.8167 (mmt) cc_final: 0.7775 (mmt) REVERT: D 587 HIS cc_start: 0.8882 (p-80) cc_final: 0.8565 (p-80) REVERT: D 590 ASP cc_start: 0.8720 (m-30) cc_final: 0.8254 (p0) outliers start: 53 outliers final: 29 residues processed: 429 average time/residue: 0.2586 time to fit residues: 177.5593 Evaluate side-chains 376 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 346 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 483 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 464 ASN B 522 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20209 Z= 0.235 Angle : 0.716 11.346 27424 Z= 0.362 Chirality : 0.042 0.155 3102 Planarity : 0.005 0.068 3454 Dihedral : 9.579 89.507 2805 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.58 % Allowed : 13.92 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.79 (0.16), residues: 2436 helix: -0.93 (0.13), residues: 1400 sheet: -2.96 (0.55), residues: 68 loop : -3.14 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 613 HIS 0.005 0.001 HIS A 258 PHE 0.017 0.001 PHE D 162 TYR 0.022 0.001 TYR C 324 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 378 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9460 (pp) cc_final: 0.9014 (pp) REVERT: A 99 MET cc_start: 0.8742 (mtp) cc_final: 0.8456 (ptp) REVERT: A 122 HIS cc_start: 0.9313 (m90) cc_final: 0.8607 (m90) REVERT: A 200 LEU cc_start: 0.9419 (mt) cc_final: 0.9211 (mt) REVERT: A 281 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 383 ASP cc_start: 0.9020 (t0) cc_final: 0.8543 (m-30) REVERT: A 440 MET cc_start: 0.9010 (tpt) cc_final: 0.8682 (tmm) REVERT: A 442 MET cc_start: 0.9001 (tpp) cc_final: 0.8710 (mmm) REVERT: A 444 LEU cc_start: 0.9553 (mp) cc_final: 0.9334 (mt) REVERT: A 515 GLU cc_start: 0.7147 (tp30) cc_final: 0.6746 (mm-30) REVERT: A 528 MET cc_start: 0.8643 (tpp) cc_final: 0.8433 (tpp) REVERT: A 577 MET cc_start: 0.8855 (tpp) cc_final: 0.8647 (tpp) REVERT: A 587 HIS cc_start: 0.8814 (p-80) cc_final: 0.8337 (p-80) REVERT: A 590 ASP cc_start: 0.8660 (m-30) cc_final: 0.8147 (p0) REVERT: A 635 ASP cc_start: 0.8645 (t0) cc_final: 0.8238 (t0) REVERT: B 122 HIS cc_start: 0.9301 (m90) cc_final: 0.8553 (m90) REVERT: B 159 LEU cc_start: 0.9409 (tp) cc_final: 0.9081 (tt) REVERT: B 281 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8753 (p) REVERT: B 345 MET cc_start: 0.8971 (tpp) cc_final: 0.8602 (tpp) REVERT: B 383 ASP cc_start: 0.8989 (t0) cc_final: 0.8501 (m-30) REVERT: B 440 MET cc_start: 0.9020 (tpt) cc_final: 0.8725 (tpp) REVERT: B 442 MET cc_start: 0.9049 (tpp) cc_final: 0.8746 (mmm) REVERT: B 444 LEU cc_start: 0.9550 (mp) cc_final: 0.9222 (mt) REVERT: B 481 MET cc_start: 0.8597 (tpp) cc_final: 0.8343 (tpp) REVERT: B 483 GLN cc_start: 0.8406 (tt0) cc_final: 0.8189 (tm-30) REVERT: B 577 MET cc_start: 0.8855 (tpp) cc_final: 0.8519 (tpp) REVERT: B 587 HIS cc_start: 0.8831 (p-80) cc_final: 0.8279 (p-80) REVERT: B 590 ASP cc_start: 0.8743 (m-30) cc_final: 0.8148 (p0) REVERT: B 603 MET cc_start: 0.8548 (ppp) cc_final: 0.8294 (ppp) REVERT: B 635 ASP cc_start: 0.8634 (t0) cc_final: 0.8175 (t0) REVERT: C 122 HIS cc_start: 0.9309 (m90) cc_final: 0.8558 (m90) REVERT: C 159 LEU cc_start: 0.9436 (tp) cc_final: 0.9126 (tt) REVERT: C 318 SER cc_start: 0.9782 (t) cc_final: 0.9539 (p) REVERT: C 383 ASP cc_start: 0.9018 (t0) cc_final: 0.8579 (m-30) REVERT: C 435 MET cc_start: 0.9170 (mmt) cc_final: 0.8262 (mmt) REVERT: C 442 MET cc_start: 0.9165 (tpp) cc_final: 0.8833 (mmm) REVERT: C 481 MET cc_start: 0.8576 (tpp) cc_final: 0.8347 (tpp) REVERT: C 515 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 578 MET cc_start: 0.8195 (mmt) cc_final: 0.7726 (mmt) REVERT: C 587 HIS cc_start: 0.8864 (p-80) cc_final: 0.8311 (p-80) REVERT: C 590 ASP cc_start: 0.8771 (m-30) cc_final: 0.8127 (p0) REVERT: C 635 ASP cc_start: 0.8651 (t0) cc_final: 0.8007 (t0) REVERT: D 66 LYS cc_start: 0.9512 (tppt) cc_final: 0.9026 (tptp) REVERT: D 178 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8946 (mm) REVERT: D 290 GLN cc_start: 0.8492 (pp30) cc_final: 0.8174 (pp30) REVERT: D 318 SER cc_start: 0.9759 (t) cc_final: 0.9502 (p) REVERT: D 331 MET cc_start: 0.8572 (tpp) cc_final: 0.7846 (tmm) REVERT: D 345 MET cc_start: 0.9031 (tpp) cc_final: 0.8767 (tpp) REVERT: D 383 ASP cc_start: 0.8962 (t0) cc_final: 0.8430 (m-30) REVERT: D 435 MET cc_start: 0.9057 (mmt) cc_final: 0.8222 (mmt) REVERT: D 440 MET cc_start: 0.9056 (tpt) cc_final: 0.8774 (tpp) REVERT: D 442 MET cc_start: 0.9114 (tpp) cc_final: 0.8816 (mmm) REVERT: D 444 LEU cc_start: 0.9575 (mp) cc_final: 0.9253 (mt) REVERT: D 466 MET cc_start: 0.9172 (mtt) cc_final: 0.8891 (mmt) REVERT: D 485 MET cc_start: 0.8396 (ttm) cc_final: 0.7667 (ttm) REVERT: D 528 MET cc_start: 0.8903 (tpp) cc_final: 0.8646 (tpp) REVERT: D 577 MET cc_start: 0.8748 (tpp) cc_final: 0.8423 (tpp) REVERT: D 578 MET cc_start: 0.8133 (mmt) cc_final: 0.7841 (mmt) REVERT: D 587 HIS cc_start: 0.8839 (p-80) cc_final: 0.8446 (p-80) REVERT: D 590 ASP cc_start: 0.8711 (m-30) cc_final: 0.8229 (p0) REVERT: D 635 ASP cc_start: 0.8597 (t0) cc_final: 0.8213 (t0) outliers start: 76 outliers final: 39 residues processed: 436 average time/residue: 0.2725 time to fit residues: 189.4723 Evaluate side-chains 384 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 342 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 0.0370 chunk 235 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20209 Z= 0.181 Angle : 0.695 11.196 27424 Z= 0.343 Chirality : 0.042 0.152 3102 Planarity : 0.004 0.066 3454 Dihedral : 9.250 89.714 2805 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.55 % Allowed : 16.51 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.40 (0.17), residues: 2436 helix: -0.52 (0.14), residues: 1388 sheet: -2.86 (0.57), residues: 68 loop : -3.11 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 613 HIS 0.004 0.001 HIS B 258 PHE 0.022 0.001 PHE D 162 TYR 0.021 0.001 TYR A 324 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 376 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9435 (pp) cc_final: 0.9180 (pp) REVERT: A 122 HIS cc_start: 0.9313 (m90) cc_final: 0.8627 (m90) REVERT: A 176 GLU cc_start: 0.9361 (pm20) cc_final: 0.9019 (pm20) REVERT: A 200 LEU cc_start: 0.9403 (mt) cc_final: 0.9192 (mt) REVERT: A 242 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9068 (t) REVERT: A 331 MET cc_start: 0.8434 (tpp) cc_final: 0.7615 (tmm) REVERT: A 383 ASP cc_start: 0.8992 (t0) cc_final: 0.8588 (m-30) REVERT: A 435 MET cc_start: 0.9060 (mmt) cc_final: 0.8055 (mmm) REVERT: A 440 MET cc_start: 0.9017 (tpt) cc_final: 0.8707 (tmm) REVERT: A 444 LEU cc_start: 0.9545 (mp) cc_final: 0.9333 (mt) REVERT: A 515 GLU cc_start: 0.7132 (tp30) cc_final: 0.6722 (mm-30) REVERT: A 528 MET cc_start: 0.8612 (tpp) cc_final: 0.8334 (tpp) REVERT: A 577 MET cc_start: 0.8786 (tpp) cc_final: 0.8485 (tpp) REVERT: A 578 MET cc_start: 0.8168 (mmt) cc_final: 0.7804 (mmt) REVERT: A 587 HIS cc_start: 0.8774 (p-80) cc_final: 0.8375 (p-80) REVERT: A 590 ASP cc_start: 0.8594 (m-30) cc_final: 0.7995 (p0) REVERT: A 635 ASP cc_start: 0.8667 (t0) cc_final: 0.8245 (t0) REVERT: B 122 HIS cc_start: 0.9284 (m90) cc_final: 0.8584 (m90) REVERT: B 159 LEU cc_start: 0.9391 (tp) cc_final: 0.9069 (tt) REVERT: B 200 LEU cc_start: 0.9412 (mt) cc_final: 0.9178 (mt) REVERT: B 246 LEU cc_start: 0.9508 (tp) cc_final: 0.9305 (tp) REVERT: B 318 SER cc_start: 0.9793 (t) cc_final: 0.9550 (p) REVERT: B 331 MET cc_start: 0.8482 (tpp) cc_final: 0.7671 (tmm) REVERT: B 383 ASP cc_start: 0.8980 (t0) cc_final: 0.8487 (m-30) REVERT: B 435 MET cc_start: 0.9088 (mmt) cc_final: 0.8121 (mmm) REVERT: B 440 MET cc_start: 0.9003 (tpt) cc_final: 0.8663 (tmm) REVERT: B 442 MET cc_start: 0.9003 (tpp) cc_final: 0.8724 (mmm) REVERT: B 444 LEU cc_start: 0.9540 (mp) cc_final: 0.9333 (mt) REVERT: B 528 MET cc_start: 0.8644 (tpp) cc_final: 0.8442 (tpp) REVERT: B 577 MET cc_start: 0.8747 (tpp) cc_final: 0.8451 (tpp) REVERT: B 578 MET cc_start: 0.8275 (mmt) cc_final: 0.7925 (mmt) REVERT: B 603 MET cc_start: 0.8597 (ppp) cc_final: 0.8341 (ppp) REVERT: B 635 ASP cc_start: 0.8624 (t0) cc_final: 0.8294 (t0) REVERT: C 122 HIS cc_start: 0.9277 (m90) cc_final: 0.8576 (m90) REVERT: C 159 LEU cc_start: 0.9404 (tp) cc_final: 0.9082 (tt) REVERT: C 232 LEU cc_start: 0.8539 (tt) cc_final: 0.8335 (tp) REVERT: C 302 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7603 (tpp-160) REVERT: C 318 SER cc_start: 0.9773 (t) cc_final: 0.9529 (p) REVERT: C 331 MET cc_start: 0.8550 (tpp) cc_final: 0.7717 (tmm) REVERT: C 383 ASP cc_start: 0.8992 (t0) cc_final: 0.8516 (m-30) REVERT: C 435 MET cc_start: 0.9047 (mmt) cc_final: 0.7990 (mmm) REVERT: C 515 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7161 (mp0) REVERT: C 577 MET cc_start: 0.8623 (tpp) cc_final: 0.8380 (tpp) REVERT: C 635 ASP cc_start: 0.8501 (t0) cc_final: 0.8170 (t0) REVERT: D 66 LYS cc_start: 0.9509 (tppt) cc_final: 0.9057 (tptp) REVERT: D 92 LEU cc_start: 0.9490 (pp) cc_final: 0.9244 (pt) REVERT: D 177 GLU cc_start: 0.9050 (pm20) cc_final: 0.8791 (pm20) REVERT: D 178 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8838 (mm) REVERT: D 318 SER cc_start: 0.9761 (t) cc_final: 0.9497 (p) REVERT: D 331 MET cc_start: 0.8549 (tpp) cc_final: 0.7815 (tmm) REVERT: D 383 ASP cc_start: 0.8921 (t0) cc_final: 0.8424 (m-30) REVERT: D 402 VAL cc_start: 0.9142 (p) cc_final: 0.8638 (p) REVERT: D 435 MET cc_start: 0.8988 (mmt) cc_final: 0.8092 (mmm) REVERT: D 440 MET cc_start: 0.9125 (tpt) cc_final: 0.8856 (tpp) REVERT: D 442 MET cc_start: 0.9053 (tpp) cc_final: 0.8791 (mmm) REVERT: D 444 LEU cc_start: 0.9574 (mp) cc_final: 0.9274 (mt) REVERT: D 466 MET cc_start: 0.9147 (mtt) cc_final: 0.8910 (mmt) REVERT: D 528 MET cc_start: 0.8818 (tpp) cc_final: 0.8460 (tpp) REVERT: D 577 MET cc_start: 0.8692 (tpp) cc_final: 0.8412 (tpp) REVERT: D 587 HIS cc_start: 0.8793 (p-80) cc_final: 0.8140 (p-80) REVERT: D 590 ASP cc_start: 0.8693 (m-30) cc_final: 0.8269 (p0) REVERT: D 635 ASP cc_start: 0.8574 (t0) cc_final: 0.8184 (t0) outliers start: 54 outliers final: 32 residues processed: 408 average time/residue: 0.2678 time to fit residues: 177.3827 Evaluate side-chains 382 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 348 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 546 ASN B 483 GLN B 546 ASN C 118 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20209 Z= 0.200 Angle : 0.708 11.286 27424 Z= 0.347 Chirality : 0.042 0.137 3102 Planarity : 0.004 0.060 3454 Dihedral : 8.850 89.953 2805 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 3.40 % Allowed : 17.03 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.21 (0.17), residues: 2436 helix: -0.39 (0.14), residues: 1388 sheet: -2.78 (0.59), residues: 68 loop : -2.98 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 613 HIS 0.006 0.001 HIS C 587 PHE 0.015 0.001 PHE B 162 TYR 0.021 0.001 TYR C 324 ARG 0.006 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 366 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7651 (mtp) cc_final: 0.7413 (mmm) REVERT: A 122 HIS cc_start: 0.9300 (m90) cc_final: 0.8567 (m90) REVERT: A 200 LEU cc_start: 0.9377 (mt) cc_final: 0.8863 (mt) REVERT: A 242 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9067 (t) REVERT: A 331 MET cc_start: 0.8485 (tpp) cc_final: 0.7668 (tmm) REVERT: A 383 ASP cc_start: 0.9044 (t0) cc_final: 0.8565 (m-30) REVERT: A 435 MET cc_start: 0.9085 (mmt) cc_final: 0.8106 (mmm) REVERT: A 440 MET cc_start: 0.9037 (tpt) cc_final: 0.8740 (tmm) REVERT: A 515 GLU cc_start: 0.7226 (tp30) cc_final: 0.6800 (mm-30) REVERT: A 528 MET cc_start: 0.8649 (tpp) cc_final: 0.8358 (tpp) REVERT: A 577 MET cc_start: 0.8758 (tpp) cc_final: 0.8418 (tpp) REVERT: A 578 MET cc_start: 0.8343 (mmt) cc_final: 0.7959 (mmt) REVERT: A 587 HIS cc_start: 0.8716 (p-80) cc_final: 0.8383 (p-80) REVERT: A 590 ASP cc_start: 0.8556 (m-30) cc_final: 0.7947 (p0) REVERT: A 635 ASP cc_start: 0.8672 (t0) cc_final: 0.8384 (t0) REVERT: B 122 HIS cc_start: 0.9231 (m90) cc_final: 0.8551 (m90) REVERT: B 159 LEU cc_start: 0.9413 (tp) cc_final: 0.9066 (tt) REVERT: B 176 GLU cc_start: 0.9392 (pm20) cc_final: 0.9034 (pm20) REVERT: B 200 LEU cc_start: 0.9383 (mt) cc_final: 0.8924 (mt) REVERT: B 246 LEU cc_start: 0.9515 (tp) cc_final: 0.9309 (tp) REVERT: B 302 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7726 (tpm170) REVERT: B 318 SER cc_start: 0.9797 (t) cc_final: 0.9548 (p) REVERT: B 331 MET cc_start: 0.8492 (tpp) cc_final: 0.7698 (tmm) REVERT: B 383 ASP cc_start: 0.8960 (t0) cc_final: 0.8511 (m-30) REVERT: B 435 MET cc_start: 0.9107 (mmt) cc_final: 0.8022 (mmm) REVERT: B 440 MET cc_start: 0.9082 (tpt) cc_final: 0.8779 (tmm) REVERT: B 444 LEU cc_start: 0.9532 (mp) cc_final: 0.9330 (mt) REVERT: B 485 MET cc_start: 0.8595 (tpp) cc_final: 0.8248 (ttm) REVERT: B 515 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 520 LEU cc_start: 0.9428 (tp) cc_final: 0.9220 (tp) REVERT: B 528 MET cc_start: 0.8677 (tpp) cc_final: 0.8367 (tpp) REVERT: B 577 MET cc_start: 0.8711 (tpp) cc_final: 0.8371 (tpp) REVERT: B 578 MET cc_start: 0.8356 (mmt) cc_final: 0.7848 (mmt) REVERT: B 603 MET cc_start: 0.8649 (ppp) cc_final: 0.8356 (ppp) REVERT: B 635 ASP cc_start: 0.8631 (t0) cc_final: 0.8359 (t0) REVERT: C 99 MET cc_start: 0.8957 (mtp) cc_final: 0.8660 (ptp) REVERT: C 122 HIS cc_start: 0.9231 (m90) cc_final: 0.8518 (m90) REVERT: C 178 ILE cc_start: 0.9620 (mp) cc_final: 0.9069 (mp) REVERT: C 232 LEU cc_start: 0.8576 (tt) cc_final: 0.8240 (tp) REVERT: C 302 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7710 (tpm170) REVERT: C 318 SER cc_start: 0.9774 (t) cc_final: 0.9515 (p) REVERT: C 331 MET cc_start: 0.8556 (tpp) cc_final: 0.7704 (tmm) REVERT: C 383 ASP cc_start: 0.8980 (t0) cc_final: 0.8505 (m-30) REVERT: C 435 MET cc_start: 0.9077 (mmt) cc_final: 0.8148 (mmm) REVERT: C 515 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7186 (mp0) REVERT: C 528 MET cc_start: 0.8717 (tpp) cc_final: 0.8501 (tpp) REVERT: C 577 MET cc_start: 0.8603 (tpp) cc_final: 0.8335 (tpp) REVERT: C 635 ASP cc_start: 0.8550 (t0) cc_final: 0.8212 (t0) REVERT: D 177 GLU cc_start: 0.9140 (pm20) cc_final: 0.8794 (pm20) REVERT: D 178 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 290 GLN cc_start: 0.8508 (pm20) cc_final: 0.8096 (mm-40) REVERT: D 318 SER cc_start: 0.9766 (t) cc_final: 0.9507 (p) REVERT: D 331 MET cc_start: 0.8581 (tpp) cc_final: 0.7817 (tmm) REVERT: D 383 ASP cc_start: 0.8891 (t0) cc_final: 0.8380 (m-30) REVERT: D 435 MET cc_start: 0.8996 (mmt) cc_final: 0.8114 (mmm) REVERT: D 440 MET cc_start: 0.9156 (tpt) cc_final: 0.8866 (tmm) REVERT: D 442 MET cc_start: 0.8987 (tpp) cc_final: 0.8777 (mmm) REVERT: D 466 MET cc_start: 0.9143 (mtt) cc_final: 0.8857 (mmt) REVERT: D 528 MET cc_start: 0.8807 (tpp) cc_final: 0.8411 (tpp) REVERT: D 577 MET cc_start: 0.8734 (tpp) cc_final: 0.8357 (tpp) REVERT: D 635 ASP cc_start: 0.8602 (t0) cc_final: 0.8292 (t0) outliers start: 72 outliers final: 49 residues processed: 410 average time/residue: 0.2638 time to fit residues: 173.4587 Evaluate side-chains 385 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 334 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 236 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20209 Z= 0.179 Angle : 0.718 13.914 27424 Z= 0.347 Chirality : 0.042 0.179 3102 Planarity : 0.004 0.060 3454 Dihedral : 8.515 89.762 2805 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.07 % Allowed : 18.92 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.91 (0.17), residues: 2436 helix: -0.12 (0.14), residues: 1368 sheet: -2.73 (0.59), residues: 68 loop : -2.85 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 613 HIS 0.006 0.001 HIS D 587 PHE 0.010 0.001 PHE D 468 TYR 0.021 0.001 TYR A 324 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 351 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7767 (mtp) cc_final: 0.7495 (mmm) REVERT: A 122 HIS cc_start: 0.9215 (m90) cc_final: 0.8532 (m90) REVERT: A 176 GLU cc_start: 0.9388 (pm20) cc_final: 0.8960 (pm20) REVERT: A 200 LEU cc_start: 0.9368 (mt) cc_final: 0.8861 (mt) REVERT: A 242 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9041 (t) REVERT: A 302 ARG cc_start: 0.8396 (tpm170) cc_final: 0.8095 (tpm170) REVERT: A 331 MET cc_start: 0.8473 (tpp) cc_final: 0.7659 (tmm) REVERT: A 383 ASP cc_start: 0.9040 (t0) cc_final: 0.8556 (m-30) REVERT: A 435 MET cc_start: 0.9074 (mmt) cc_final: 0.8071 (mmm) REVERT: A 440 MET cc_start: 0.9055 (tpt) cc_final: 0.8813 (tmm) REVERT: A 515 GLU cc_start: 0.7171 (tp30) cc_final: 0.6796 (mm-30) REVERT: A 528 MET cc_start: 0.8557 (tpp) cc_final: 0.8208 (tpp) REVERT: A 577 MET cc_start: 0.8692 (tpp) cc_final: 0.8347 (tpp) REVERT: A 578 MET cc_start: 0.8395 (mmt) cc_final: 0.7971 (mmt) REVERT: A 635 ASP cc_start: 0.8668 (t0) cc_final: 0.8373 (t0) REVERT: B 99 MET cc_start: 0.9187 (ptp) cc_final: 0.8645 (ptp) REVERT: B 118 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 122 HIS cc_start: 0.9239 (m90) cc_final: 0.8435 (m90) REVERT: B 159 LEU cc_start: 0.9394 (tp) cc_final: 0.9072 (tt) REVERT: B 200 LEU cc_start: 0.9356 (mt) cc_final: 0.8855 (mt) REVERT: B 232 LEU cc_start: 0.8523 (tt) cc_final: 0.8167 (tp) REVERT: B 242 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9066 (t) REVERT: B 302 ARG cc_start: 0.8103 (tpp-160) cc_final: 0.7842 (tpm170) REVERT: B 318 SER cc_start: 0.9793 (t) cc_final: 0.9546 (p) REVERT: B 331 MET cc_start: 0.8534 (tpp) cc_final: 0.7704 (tmm) REVERT: B 383 ASP cc_start: 0.8950 (t0) cc_final: 0.8555 (m-30) REVERT: B 435 MET cc_start: 0.9056 (mmt) cc_final: 0.8116 (mmm) REVERT: B 440 MET cc_start: 0.9116 (tpt) cc_final: 0.8825 (tmm) REVERT: B 444 LEU cc_start: 0.9527 (mp) cc_final: 0.9327 (mt) REVERT: B 474 MET cc_start: 0.8909 (tpp) cc_final: 0.8608 (tpp) REVERT: B 515 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 528 MET cc_start: 0.8602 (tpp) cc_final: 0.8256 (tpp) REVERT: B 577 MET cc_start: 0.8678 (tpp) cc_final: 0.8406 (tpp) REVERT: B 578 MET cc_start: 0.8383 (mmt) cc_final: 0.7965 (mmt) REVERT: B 603 MET cc_start: 0.8681 (ppp) cc_final: 0.8381 (ppp) REVERT: B 635 ASP cc_start: 0.8673 (t0) cc_final: 0.8331 (t0) REVERT: C 99 MET cc_start: 0.8982 (mtp) cc_final: 0.8631 (ptp) REVERT: C 122 HIS cc_start: 0.9215 (m90) cc_final: 0.8538 (m90) REVERT: C 173 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8463 (p) REVERT: C 176 GLU cc_start: 0.9485 (pm20) cc_final: 0.9096 (mp0) REVERT: C 177 GLU cc_start: 0.9026 (pm20) cc_final: 0.8580 (pm20) REVERT: C 215 MET cc_start: 0.8707 (mmt) cc_final: 0.8479 (mmp) REVERT: C 242 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9013 (t) REVERT: C 302 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7746 (tpm170) REVERT: C 318 SER cc_start: 0.9768 (t) cc_final: 0.9506 (p) REVERT: C 331 MET cc_start: 0.8534 (tpp) cc_final: 0.7708 (tmm) REVERT: C 383 ASP cc_start: 0.8996 (t0) cc_final: 0.8471 (m-30) REVERT: C 435 MET cc_start: 0.9087 (mmt) cc_final: 0.8147 (mmm) REVERT: C 474 MET cc_start: 0.8929 (tpp) cc_final: 0.8621 (tpp) REVERT: C 515 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7067 (mp0) REVERT: C 528 MET cc_start: 0.8687 (tpp) cc_final: 0.8403 (tpp) REVERT: C 577 MET cc_start: 0.8508 (tpp) cc_final: 0.8286 (tpp) REVERT: C 635 ASP cc_start: 0.8549 (t0) cc_final: 0.8216 (t0) REVERT: D 29 TRP cc_start: 0.6879 (t-100) cc_final: 0.6486 (t60) REVERT: D 66 LYS cc_start: 0.9111 (mttt) cc_final: 0.8872 (mttp) REVERT: D 177 GLU cc_start: 0.9196 (pm20) cc_final: 0.8928 (pm20) REVERT: D 178 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8757 (mm) REVERT: D 290 GLN cc_start: 0.8435 (pm20) cc_final: 0.8010 (mm-40) REVERT: D 318 SER cc_start: 0.9764 (t) cc_final: 0.9506 (p) REVERT: D 331 MET cc_start: 0.8561 (tpp) cc_final: 0.7797 (tmm) REVERT: D 383 ASP cc_start: 0.8874 (t0) cc_final: 0.8379 (m-30) REVERT: D 435 MET cc_start: 0.8976 (mmt) cc_final: 0.7960 (mmt) REVERT: D 440 MET cc_start: 0.9191 (tpt) cc_final: 0.8975 (tmm) REVERT: D 442 MET cc_start: 0.8951 (tpp) cc_final: 0.8750 (mmm) REVERT: D 466 MET cc_start: 0.9181 (mtt) cc_final: 0.8920 (mmm) REVERT: D 528 MET cc_start: 0.8729 (tpp) cc_final: 0.8328 (tpp) REVERT: D 635 ASP cc_start: 0.8592 (t0) cc_final: 0.8281 (t0) outliers start: 65 outliers final: 43 residues processed: 393 average time/residue: 0.2580 time to fit residues: 163.5908 Evaluate side-chains 391 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 342 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20209 Z= 0.189 Angle : 0.730 11.563 27424 Z= 0.350 Chirality : 0.042 0.201 3102 Planarity : 0.004 0.054 3454 Dihedral : 8.298 89.864 2805 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.92 % Allowed : 19.58 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.93 (0.17), residues: 2436 helix: -0.15 (0.14), residues: 1408 sheet: -2.77 (0.59), residues: 68 loop : -2.94 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 629 HIS 0.006 0.001 HIS A 587 PHE 0.010 0.001 PHE B 211 TYR 0.022 0.001 TYR A 324 ARG 0.005 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 346 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9253 (ppp) cc_final: 0.8997 (ppp) REVERT: A 99 MET cc_start: 0.9106 (ptp) cc_final: 0.8435 (ptp) REVERT: A 110 MET cc_start: 0.7785 (mtp) cc_final: 0.7569 (mmm) REVERT: A 122 HIS cc_start: 0.9209 (m90) cc_final: 0.8764 (m-70) REVERT: A 176 GLU cc_start: 0.9354 (pm20) cc_final: 0.9091 (pm20) REVERT: A 200 LEU cc_start: 0.9375 (mt) cc_final: 0.8900 (mt) REVERT: A 242 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9031 (t) REVERT: A 302 ARG cc_start: 0.8400 (tpm170) cc_final: 0.8063 (tpm170) REVERT: A 331 MET cc_start: 0.8518 (tpp) cc_final: 0.7692 (tmm) REVERT: A 383 ASP cc_start: 0.9044 (t0) cc_final: 0.8561 (m-30) REVERT: A 435 MET cc_start: 0.9060 (mmt) cc_final: 0.8083 (mmm) REVERT: A 440 MET cc_start: 0.9043 (tpt) cc_final: 0.8828 (tmm) REVERT: A 515 GLU cc_start: 0.7247 (tp30) cc_final: 0.6884 (mm-30) REVERT: A 528 MET cc_start: 0.8677 (tpp) cc_final: 0.8351 (tpp) REVERT: A 577 MET cc_start: 0.8660 (tpp) cc_final: 0.8314 (tpp) REVERT: A 578 MET cc_start: 0.8402 (mmt) cc_final: 0.7976 (mmt) REVERT: A 635 ASP cc_start: 0.8676 (t0) cc_final: 0.8316 (t0) REVERT: B 118 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: B 122 HIS cc_start: 0.9218 (m90) cc_final: 0.8472 (m90) REVERT: B 159 LEU cc_start: 0.9393 (tp) cc_final: 0.9056 (tt) REVERT: B 176 GLU cc_start: 0.9399 (pm20) cc_final: 0.9067 (pm20) REVERT: B 200 LEU cc_start: 0.9357 (mt) cc_final: 0.8884 (mt) REVERT: B 232 LEU cc_start: 0.8546 (tt) cc_final: 0.8199 (tp) REVERT: B 242 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 302 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7773 (tpm170) REVERT: B 318 SER cc_start: 0.9797 (t) cc_final: 0.9545 (p) REVERT: B 331 MET cc_start: 0.8516 (tpp) cc_final: 0.7697 (tmm) REVERT: B 383 ASP cc_start: 0.9012 (t0) cc_final: 0.8499 (m-30) REVERT: B 435 MET cc_start: 0.9013 (mmt) cc_final: 0.8085 (mmm) REVERT: B 440 MET cc_start: 0.9055 (tpt) cc_final: 0.8791 (tmm) REVERT: B 528 MET cc_start: 0.8622 (tpp) cc_final: 0.8259 (tpp) REVERT: B 577 MET cc_start: 0.8708 (tpp) cc_final: 0.8370 (tpp) REVERT: B 578 MET cc_start: 0.8344 (mmt) cc_final: 0.8004 (mmt) REVERT: B 603 MET cc_start: 0.8700 (ppp) cc_final: 0.8415 (ppp) REVERT: B 635 ASP cc_start: 0.8678 (t0) cc_final: 0.8392 (t0) REVERT: C 99 MET cc_start: 0.9040 (mtp) cc_final: 0.8699 (ptp) REVERT: C 122 HIS cc_start: 0.9194 (m90) cc_final: 0.8480 (m90) REVERT: C 173 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 176 GLU cc_start: 0.9481 (pm20) cc_final: 0.9078 (mp0) REVERT: C 177 GLU cc_start: 0.9077 (pm20) cc_final: 0.8623 (pm20) REVERT: C 178 ILE cc_start: 0.9539 (mp) cc_final: 0.8931 (mp) REVERT: C 215 MET cc_start: 0.8683 (mmt) cc_final: 0.8448 (mmp) REVERT: C 242 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9003 (t) REVERT: C 302 ARG cc_start: 0.8113 (tpp-160) cc_final: 0.7820 (tpm170) REVERT: C 318 SER cc_start: 0.9778 (t) cc_final: 0.9518 (p) REVERT: C 331 MET cc_start: 0.8518 (tpp) cc_final: 0.7698 (tmm) REVERT: C 383 ASP cc_start: 0.8996 (t0) cc_final: 0.8651 (m-30) REVERT: C 435 MET cc_start: 0.9053 (mmt) cc_final: 0.8135 (mmm) REVERT: C 515 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 528 MET cc_start: 0.8706 (tpp) cc_final: 0.8402 (tpp) REVERT: C 577 MET cc_start: 0.8569 (tpp) cc_final: 0.8267 (tpp) REVERT: C 635 ASP cc_start: 0.8548 (t0) cc_final: 0.8266 (t0) REVERT: D 96 MET cc_start: 0.9422 (ptp) cc_final: 0.9032 (ptp) REVERT: D 177 GLU cc_start: 0.9237 (pm20) cc_final: 0.9015 (pm20) REVERT: D 178 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.8742 (mm) REVERT: D 290 GLN cc_start: 0.8421 (pm20) cc_final: 0.7968 (mm-40) REVERT: D 318 SER cc_start: 0.9765 (t) cc_final: 0.9509 (p) REVERT: D 331 MET cc_start: 0.8566 (tpp) cc_final: 0.7789 (tmm) REVERT: D 383 ASP cc_start: 0.8870 (t0) cc_final: 0.8366 (m-30) REVERT: D 435 MET cc_start: 0.8984 (mmt) cc_final: 0.7964 (mmt) REVERT: D 466 MET cc_start: 0.9207 (mtt) cc_final: 0.8900 (mmm) REVERT: D 528 MET cc_start: 0.8689 (tpp) cc_final: 0.8285 (tpp) REVERT: D 635 ASP cc_start: 0.8628 (t0) cc_final: 0.8309 (t0) outliers start: 62 outliers final: 45 residues processed: 384 average time/residue: 0.2672 time to fit residues: 165.0801 Evaluate side-chains 388 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 337 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 128 GLN A 158 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20209 Z= 0.341 Angle : 0.812 11.248 27424 Z= 0.397 Chirality : 0.046 0.201 3102 Planarity : 0.004 0.047 3454 Dihedral : 8.768 89.637 2805 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.58 % Allowed : 19.34 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2436 helix: -0.18 (0.14), residues: 1404 sheet: -2.86 (0.59), residues: 68 loop : -2.90 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.005 0.001 HIS B 258 PHE 0.012 0.001 PHE D 468 TYR 0.020 0.002 TYR C 324 ARG 0.004 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 339 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7886 (mtp) cc_final: 0.7614 (mmm) REVERT: A 242 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9113 (t) REVERT: A 302 ARG cc_start: 0.8328 (tpm170) cc_final: 0.7974 (tpm170) REVERT: A 331 MET cc_start: 0.8621 (tpp) cc_final: 0.7827 (tmm) REVERT: A 383 ASP cc_start: 0.9081 (t0) cc_final: 0.8600 (m-30) REVERT: A 435 MET cc_start: 0.9026 (mmt) cc_final: 0.8000 (mmt) REVERT: A 440 MET cc_start: 0.9043 (tpt) cc_final: 0.8842 (tmm) REVERT: A 528 MET cc_start: 0.8888 (tpp) cc_final: 0.8582 (tpp) REVERT: A 577 MET cc_start: 0.8847 (tpp) cc_final: 0.8452 (tpp) REVERT: A 635 ASP cc_start: 0.8692 (t0) cc_final: 0.8350 (t0) REVERT: B 96 MET cc_start: 0.9137 (ppp) cc_final: 0.8904 (pmm) REVERT: B 122 HIS cc_start: 0.9237 (m90) cc_final: 0.8799 (m-70) REVERT: B 242 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9121 (t) REVERT: B 302 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7342 (tpm170) REVERT: B 331 MET cc_start: 0.8603 (tpp) cc_final: 0.7805 (tmm) REVERT: B 383 ASP cc_start: 0.9009 (t0) cc_final: 0.8507 (m-30) REVERT: B 435 MET cc_start: 0.9048 (mmt) cc_final: 0.8073 (mmm) REVERT: B 440 MET cc_start: 0.9137 (tpt) cc_final: 0.8935 (tmm) REVERT: B 528 MET cc_start: 0.8848 (tpp) cc_final: 0.8546 (tpp) REVERT: B 577 MET cc_start: 0.8866 (tpp) cc_final: 0.8389 (tpp) REVERT: B 603 MET cc_start: 0.8750 (ppp) cc_final: 0.8458 (ppp) REVERT: B 635 ASP cc_start: 0.8706 (t0) cc_final: 0.8318 (t0) REVERT: C 122 HIS cc_start: 0.9226 (m90) cc_final: 0.8511 (m90) REVERT: C 242 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9120 (t) REVERT: C 302 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7740 (tpp-160) REVERT: C 331 MET cc_start: 0.8625 (tpp) cc_final: 0.7825 (tmm) REVERT: C 383 ASP cc_start: 0.9018 (t0) cc_final: 0.8566 (m-30) REVERT: C 435 MET cc_start: 0.9122 (mmt) cc_final: 0.8141 (mmm) REVERT: C 515 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 577 MET cc_start: 0.8754 (tpp) cc_final: 0.8444 (tpp) REVERT: C 635 ASP cc_start: 0.8652 (t0) cc_final: 0.8383 (t0) REVERT: D 178 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9036 (mm) REVERT: D 246 LEU cc_start: 0.9523 (tp) cc_final: 0.9284 (tp) REVERT: D 290 GLN cc_start: 0.8364 (pm20) cc_final: 0.7996 (mm110) REVERT: D 318 SER cc_start: 0.9782 (t) cc_final: 0.9532 (p) REVERT: D 331 MET cc_start: 0.8626 (tpp) cc_final: 0.7865 (tmm) REVERT: D 383 ASP cc_start: 0.8920 (t0) cc_final: 0.8414 (m-30) REVERT: D 466 MET cc_start: 0.9305 (mtt) cc_final: 0.8936 (mmm) REVERT: D 528 MET cc_start: 0.8875 (tpp) cc_final: 0.8550 (tpp) REVERT: D 635 ASP cc_start: 0.8654 (t0) cc_final: 0.8372 (t0) outliers start: 76 outliers final: 56 residues processed: 388 average time/residue: 0.2563 time to fit residues: 160.9766 Evaluate side-chains 390 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9980 chunk 225 optimal weight: 0.0980 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 201 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20209 Z= 0.206 Angle : 0.785 12.207 27424 Z= 0.376 Chirality : 0.044 0.201 3102 Planarity : 0.004 0.051 3454 Dihedral : 8.334 85.288 2805 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.31 % Allowed : 21.08 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.64 (0.18), residues: 2436 helix: 0.12 (0.14), residues: 1368 sheet: -2.78 (0.59), residues: 68 loop : -2.75 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 629 HIS 0.005 0.001 HIS A 587 PHE 0.013 0.001 PHE C 211 TYR 0.020 0.001 TYR C 324 ARG 0.007 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 347 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7888 (mtp) cc_final: 0.7617 (mmm) REVERT: A 176 GLU cc_start: 0.9298 (pm20) cc_final: 0.8985 (pm20) REVERT: A 242 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9055 (t) REVERT: A 302 ARG cc_start: 0.8410 (tpm170) cc_final: 0.8051 (tpm170) REVERT: A 331 MET cc_start: 0.8548 (tpp) cc_final: 0.7743 (tmm) REVERT: A 383 ASP cc_start: 0.9090 (t0) cc_final: 0.8580 (m-30) REVERT: A 435 MET cc_start: 0.8949 (mmt) cc_final: 0.7885 (mmt) REVERT: A 528 MET cc_start: 0.8767 (tpp) cc_final: 0.8459 (tpp) REVERT: A 577 MET cc_start: 0.8815 (tpp) cc_final: 0.8347 (tpp) REVERT: A 578 MET cc_start: 0.8391 (mmt) cc_final: 0.7949 (mmt) REVERT: A 635 ASP cc_start: 0.8588 (t0) cc_final: 0.8196 (t0) REVERT: B 110 MET cc_start: 0.7831 (mtp) cc_final: 0.6942 (mmt) REVERT: B 122 HIS cc_start: 0.9255 (m90) cc_final: 0.8582 (m90) REVERT: B 176 GLU cc_start: 0.9314 (pm20) cc_final: 0.8985 (pm20) REVERT: B 242 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9071 (t) REVERT: B 302 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7895 (tpp-160) REVERT: B 331 MET cc_start: 0.8545 (tpp) cc_final: 0.7764 (tmm) REVERT: B 383 ASP cc_start: 0.9020 (t0) cc_final: 0.8501 (m-30) REVERT: B 435 MET cc_start: 0.8981 (mmt) cc_final: 0.7951 (mmm) REVERT: B 528 MET cc_start: 0.8687 (tpp) cc_final: 0.8315 (tpp) REVERT: B 577 MET cc_start: 0.8730 (tpp) cc_final: 0.8252 (tpp) REVERT: B 578 MET cc_start: 0.8416 (mmt) cc_final: 0.7943 (mmt) REVERT: B 603 MET cc_start: 0.8781 (ppp) cc_final: 0.8526 (ppp) REVERT: B 635 ASP cc_start: 0.8654 (t0) cc_final: 0.8298 (t0) REVERT: C 99 MET cc_start: 0.9063 (mtp) cc_final: 0.8861 (ptp) REVERT: C 122 HIS cc_start: 0.9204 (m90) cc_final: 0.8769 (m-70) REVERT: C 177 GLU cc_start: 0.9248 (pm20) cc_final: 0.8907 (pm20) REVERT: C 242 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9054 (t) REVERT: C 302 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7765 (tpp-160) REVERT: C 318 SER cc_start: 0.9785 (t) cc_final: 0.9530 (p) REVERT: C 331 MET cc_start: 0.8536 (tpp) cc_final: 0.7749 (tmm) REVERT: C 383 ASP cc_start: 0.9002 (t0) cc_final: 0.8545 (m-30) REVERT: C 435 MET cc_start: 0.9088 (mmt) cc_final: 0.8077 (mmm) REVERT: C 485 MET cc_start: 0.9036 (tpp) cc_final: 0.8714 (ttm) REVERT: C 515 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7240 (mm-30) REVERT: C 577 MET cc_start: 0.8644 (tpp) cc_final: 0.7976 (tpp) REVERT: C 635 ASP cc_start: 0.8607 (t0) cc_final: 0.8228 (t0) REVERT: D 66 LYS cc_start: 0.9156 (mttt) cc_final: 0.8927 (mttp) REVERT: D 110 MET cc_start: 0.7567 (mtp) cc_final: 0.6891 (mmt) REVERT: D 178 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9118 (mm) REVERT: D 318 SER cc_start: 0.9763 (t) cc_final: 0.9517 (p) REVERT: D 331 MET cc_start: 0.8540 (tpp) cc_final: 0.7794 (tmm) REVERT: D 383 ASP cc_start: 0.8854 (t0) cc_final: 0.8372 (m-30) REVERT: D 435 MET cc_start: 0.8970 (mmt) cc_final: 0.7937 (mmt) REVERT: D 466 MET cc_start: 0.9311 (mtt) cc_final: 0.8896 (mmm) REVERT: D 528 MET cc_start: 0.8707 (tpp) cc_final: 0.8291 (tpp) REVERT: D 635 ASP cc_start: 0.8639 (t0) cc_final: 0.8264 (t0) outliers start: 49 outliers final: 39 residues processed: 378 average time/residue: 0.2620 time to fit residues: 160.2328 Evaluate side-chains 371 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 328 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0570 chunk 231 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 20 optimal weight: 0.0050 chunk 149 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20209 Z= 0.193 Angle : 0.790 11.736 27424 Z= 0.375 Chirality : 0.044 0.209 3102 Planarity : 0.004 0.050 3454 Dihedral : 8.003 87.422 2805 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.12 % Allowed : 21.23 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.61 (0.18), residues: 2436 helix: 0.15 (0.15), residues: 1368 sheet: -2.82 (0.59), residues: 68 loop : -2.74 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 629 HIS 0.004 0.001 HIS A 587 PHE 0.011 0.001 PHE D 256 TYR 0.022 0.001 TYR C 324 ARG 0.008 0.000 ARG D 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 346 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8876 (ptp) cc_final: 0.8510 (ptt) REVERT: A 176 GLU cc_start: 0.9313 (pm20) cc_final: 0.8935 (pm20) REVERT: A 242 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9017 (t) REVERT: A 302 ARG cc_start: 0.8432 (tpm170) cc_final: 0.8080 (tpm170) REVERT: A 331 MET cc_start: 0.8533 (tpp) cc_final: 0.7728 (tmm) REVERT: A 383 ASP cc_start: 0.9069 (t0) cc_final: 0.8594 (m-30) REVERT: A 403 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 435 MET cc_start: 0.8937 (mmt) cc_final: 0.7888 (mmt) REVERT: A 528 MET cc_start: 0.8804 (tpp) cc_final: 0.8490 (tpp) REVERT: A 577 MET cc_start: 0.8748 (tpp) cc_final: 0.8280 (tpp) REVERT: A 635 ASP cc_start: 0.8657 (t0) cc_final: 0.8234 (t0) REVERT: B 99 MET cc_start: 0.8786 (ptp) cc_final: 0.8485 (ptt) REVERT: B 110 MET cc_start: 0.7805 (mtp) cc_final: 0.7340 (mmm) REVERT: B 113 GLU cc_start: 0.9290 (tt0) cc_final: 0.9020 (tp30) REVERT: B 176 GLU cc_start: 0.9360 (pm20) cc_final: 0.8900 (pm20) REVERT: B 242 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9044 (t) REVERT: B 260 MET cc_start: 0.8947 (mmm) cc_final: 0.8656 (tpp) REVERT: B 302 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7919 (tpp-160) REVERT: B 318 SER cc_start: 0.9793 (t) cc_final: 0.9535 (p) REVERT: B 331 MET cc_start: 0.8538 (tpp) cc_final: 0.7735 (tmm) REVERT: B 345 MET cc_start: 0.8821 (tpp) cc_final: 0.8599 (tpp) REVERT: B 383 ASP cc_start: 0.9010 (t0) cc_final: 0.8521 (m-30) REVERT: B 403 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: B 435 MET cc_start: 0.9004 (mmt) cc_final: 0.8011 (mmm) REVERT: B 528 MET cc_start: 0.8675 (tpp) cc_final: 0.8294 (tpp) REVERT: B 577 MET cc_start: 0.8669 (tpp) cc_final: 0.8183 (tpp) REVERT: B 603 MET cc_start: 0.8792 (ppp) cc_final: 0.8527 (ppp) REVERT: B 635 ASP cc_start: 0.8681 (t0) cc_final: 0.8417 (t0) REVERT: C 99 MET cc_start: 0.9135 (mtp) cc_final: 0.8487 (ptp) REVERT: C 113 GLU cc_start: 0.9290 (tt0) cc_final: 0.9046 (tp30) REVERT: C 122 HIS cc_start: 0.9165 (m90) cc_final: 0.8440 (m90) REVERT: C 177 GLU cc_start: 0.9236 (pm20) cc_final: 0.8876 (pm20) REVERT: C 242 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9016 (t) REVERT: C 302 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7819 (tpp-160) REVERT: C 318 SER cc_start: 0.9784 (t) cc_final: 0.9527 (p) REVERT: C 331 MET cc_start: 0.8560 (tpp) cc_final: 0.7727 (tmm) REVERT: C 383 ASP cc_start: 0.9016 (t0) cc_final: 0.8507 (m-30) REVERT: C 435 MET cc_start: 0.9078 (mmt) cc_final: 0.8084 (mmm) REVERT: C 515 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 577 MET cc_start: 0.8603 (tpp) cc_final: 0.7949 (tpp) REVERT: C 635 ASP cc_start: 0.8602 (t0) cc_final: 0.8222 (t0) REVERT: D 29 TRP cc_start: 0.7033 (t-100) cc_final: 0.6646 (t60) REVERT: D 66 LYS cc_start: 0.9156 (mttt) cc_final: 0.8927 (mttp) REVERT: D 110 MET cc_start: 0.7523 (mtp) cc_final: 0.6808 (mmt) REVERT: D 178 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9051 (mm) REVERT: D 290 GLN cc_start: 0.8355 (pm20) cc_final: 0.7993 (mm110) REVERT: D 318 SER cc_start: 0.9764 (t) cc_final: 0.9517 (p) REVERT: D 331 MET cc_start: 0.8540 (tpp) cc_final: 0.7763 (tmm) REVERT: D 383 ASP cc_start: 0.8935 (t0) cc_final: 0.8554 (m-30) REVERT: D 390 LEU cc_start: 0.9445 (mm) cc_final: 0.9191 (mm) REVERT: D 435 MET cc_start: 0.8954 (mmt) cc_final: 0.7934 (mmt) REVERT: D 466 MET cc_start: 0.9279 (mtt) cc_final: 0.8869 (mmm) REVERT: D 528 MET cc_start: 0.8694 (tpp) cc_final: 0.8274 (tpp) REVERT: D 577 MET cc_start: 0.8376 (tpp) cc_final: 0.8100 (tpp) REVERT: D 635 ASP cc_start: 0.8617 (t0) cc_final: 0.8341 (t0) outliers start: 45 outliers final: 39 residues processed: 374 average time/residue: 0.2640 time to fit residues: 160.4936 Evaluate side-chains 375 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 331 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 HIS Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 193 optimal weight: 10.0000 chunk 81 optimal weight: 0.0050 chunk 199 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN D 74 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.100463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078603 restraints weight = 53434.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081880 restraints weight = 26234.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084115 restraints weight = 16124.875| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20209 Z= 0.185 Angle : 0.797 12.193 27424 Z= 0.376 Chirality : 0.043 0.210 3102 Planarity : 0.004 0.051 3454 Dihedral : 7.506 86.776 2805 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.89 % Allowed : 21.51 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.60 (0.17), residues: 2436 helix: 0.11 (0.14), residues: 1376 sheet: -2.74 (0.58), residues: 68 loop : -2.68 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 629 HIS 0.004 0.001 HIS A 587 PHE 0.011 0.001 PHE B 211 TYR 0.022 0.001 TYR C 324 ARG 0.006 0.000 ARG D 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4201.54 seconds wall clock time: 77 minutes 34.43 seconds (4654.43 seconds total)