Starting phenix.real_space_refine on Mon Dec 30 22:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr0_14875/12_2024/7zr0_14875.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 73 5.16 5 C 8870 2.51 5 N 2388 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5132 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5112 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2243 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain: "K" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1503 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.82, per 1000 atoms: 0.70 Number of scatterers: 14052 At special positions: 0 Unit cell: (118.68, 126.42, 139.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 7 15.00 O 2714 8.00 N 2388 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 44.8% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.049A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.822A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.944A pdb=" N ILE A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.552A pdb=" N TYR A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 420 removed outlier: 4.231A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.059A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.847A pdb=" N GLY A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.991A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.826A pdb=" N GLY A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.845A pdb=" N GLU A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 removed outlier: 3.590A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.691A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 618 removed outlier: 4.680A pdb=" N MET A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 632 through 645 removed outlier: 4.106A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 687 removed outlier: 3.578A pdb=" N SER A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.733A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.782A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.225A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.676A pdb=" N SER B 135 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 342 through 346 removed outlier: 4.307A pdb=" N ASN B 346 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 420 removed outlier: 3.888A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.311A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.530A pdb=" N VAL B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 475' Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.412A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 560 Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.538A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.912A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.570A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 687 removed outlier: 4.095A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 72 removed outlier: 3.953A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 112 removed outlier: 3.642A pdb=" N LYS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.840A pdb=" N LEU C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 119' Processing helix chain 'C' and resid 139 through 164 removed outlier: 4.101A pdb=" N MET C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 182 Processing helix chain 'C' and resid 183 through 201 removed outlier: 3.521A pdb=" N ALA C 187 " --> pdb=" O CYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 227 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.580A pdb=" N THR C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 266 Processing helix chain 'K' and resid 536 through 543 removed outlier: 3.572A pdb=" N HIS K 540 " --> pdb=" O SER K 536 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 568 removed outlier: 3.514A pdb=" N LEU K 553 " --> pdb=" O GLU K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 652 removed outlier: 3.741A pdb=" N ASP K 638 " --> pdb=" O SER K 634 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 through 671 Processing helix chain 'K' and resid 687 through 697 removed outlier: 3.786A pdb=" N LEU K 697 " --> pdb=" O MET K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 719 removed outlier: 3.639A pdb=" N ILE K 710 " --> pdb=" O LEU K 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.669A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 165 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.878A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 159 removed outlier: 3.833A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.714A pdb=" N ILE A 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 324 removed outlier: 3.859A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 378 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS A 354 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 383 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 356 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.935A pdb=" N TYR A 484 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N MET A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 486 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 580 removed outlier: 7.410A pdb=" N THR A 579 " --> pdb=" O ILE A 628 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.707A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 334 through 335 removed outlier: 3.532A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330 removed outlier: 3.691A pdb=" N PHE B 329 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 364 removed outlier: 7.324A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 462 through 468 removed outlier: 6.969A pdb=" N GLU B 465 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR B 459 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 575 through 580 removed outlier: 6.388A pdb=" N LYS B 624 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1614 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: 3.93 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 1 1.05 - 1.24: 1742 1.24 - 1.43: 4127 1.43 - 1.62: 8299 1.62 - 1.81: 124 Bond restraints: 14293 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 0.858 0.634 5.00e-02 4.00e+02 1.61e+02 bond pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.503 1.257 0.246 3.40e-02 8.65e+02 5.25e+01 bond pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.80e+01 bond pdb=" N PRO B 79 " pdb=" CD PRO B 79 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.26e+01 bond pdb=" C MET C 112 " pdb=" N PRO C 113 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.25e-02 6.40e+03 9.40e+00 ... (remaining 14288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 19213 14.77 - 29.54: 2 29.54 - 44.31: 0 44.31 - 59.08: 0 59.08 - 73.85: 1 Bond angle restraints: 19216 Sorted by residual: angle pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO A 79 " pdb=" CD PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 103.20 78.91 24.29 1.50e+00 4.44e-01 2.62e+02 angle pdb=" CA PRO A 79 " pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 104.50 77.07 27.43 1.90e+00 2.77e-01 2.08e+02 angle pdb=" N ILE A 690 " pdb=" CA ILE A 690 " pdb=" C ILE A 690 " ideal model delta sigma weight residual 112.96 107.29 5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 104.27 7.73 1.40e+00 5.10e-01 3.05e+01 ... (remaining 19211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7155 17.95 - 35.90: 1276 35.90 - 53.85: 353 53.85 - 71.80: 65 71.80 - 89.74: 30 Dihedral angle restraints: 8879 sinusoidal: 3826 harmonic: 5053 Sorted by residual: dihedral pdb=" CA THR B 309 " pdb=" C THR B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA MET C 112 " pdb=" C MET C 112 " pdb=" N PRO C 113 " pdb=" CA PRO C 113 " ideal model delta harmonic sigma weight residual 180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" N PRO A 79 " pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " pdb=" CB PRO A 79 " ideal model delta sinusoidal sigma weight residual -30.00 -112.14 82.14 1 1.50e+01 4.44e-03 3.68e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1476 0.043 - 0.086: 483 0.086 - 0.130: 126 0.130 - 0.173: 18 0.173 - 0.216: 5 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA PRO K 523 " pdb=" N PRO K 523 " pdb=" C PRO K 523 " pdb=" CB PRO K 523 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU B 539 " pdb=" N GLU B 539 " pdb=" C GLU B 539 " pdb=" CB GLU B 539 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR B 190 " pdb=" CA THR B 190 " pdb=" OG1 THR B 190 " pdb=" CG2 THR B 190 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2105 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 173 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.25e+01 pdb=" N PRO B 174 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 20 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO C 21 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 9 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C HIS C 9 " 0.048 2.00e-02 2.50e+03 pdb=" O HIS C 9 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 10 " -0.016 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 137 2.59 - 3.17: 11270 3.17 - 3.74: 19896 3.74 - 4.32: 25260 4.32 - 4.90: 43624 Nonbonded interactions: 100187 Sorted by model distance: nonbonded pdb=" OG1 THR B 94 " pdb=" OD2 ASP B 152 " model vdw 2.011 3.040 nonbonded pdb=" O ILE A 690 " pdb=" OE1 GLU A 692 " model vdw 2.119 3.040 nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.129 3.040 nonbonded pdb=" O SER B 160 " pdb=" OG SER B 160 " model vdw 2.182 3.040 nonbonded pdb=" N GLU A 542 " pdb=" OE1 GLU A 542 " model vdw 2.197 3.120 ... (remaining 100182 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 10 through 220 or resid 273 through 692 or resid 801)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.980 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.007 0.634 14293 Z= 0.333 Angle : 0.995 73.851 19216 Z= 0.497 Chirality : 0.046 0.216 2108 Planarity : 0.006 0.118 2455 Dihedral : 19.990 89.744 5595 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.06 % Favored : 89.35 % Rotamer: Outliers : 0.19 % Allowed : 35.74 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % 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: -2.37 (0.19), residues: 1699 helix: 0.39 (0.20), residues: 719 sheet: -2.11 (0.36), residues: 199 loop : -3.47 (0.18), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 114 HIS 0.009 0.002 HIS A 632 PHE 0.023 0.002 PHE B 165 TYR 0.026 0.002 TYR A 137 ARG 0.010 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 1.642 Fit side-chains REVERT: B 52 ASP cc_start: 0.8359 (t0) cc_final: 0.8020 (m-30) outliers start: 3 outliers final: 2 residues processed: 299 average time/residue: 0.3179 time to fit residues: 132.3116 Evaluate side-chains 298 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 7.9990 chunk 128 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 68 optimal weight: 0.0020 chunk 133 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 101 ASN B 320 HIS B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14293 Z= 0.188 Angle : 0.647 12.908 19216 Z= 0.342 Chirality : 0.043 0.208 2108 Planarity : 0.005 0.077 2455 Dihedral : 7.188 81.372 1936 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.83 % Favored : 90.70 % Rotamer: Outliers : 3.16 % Allowed : 32.65 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1699 helix: 0.84 (0.20), residues: 727 sheet: -1.71 (0.39), residues: 185 loop : -3.24 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 114 HIS 0.004 0.001 HIS B 676 PHE 0.012 0.001 PHE B 165 TYR 0.013 0.001 TYR A 134 ARG 0.004 0.000 ARG K 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 1.766 Fit side-chains REVERT: A 137 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6171 (t80) REVERT: A 303 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 491 LYS cc_start: 0.8323 (tmtt) cc_final: 0.8071 (tttm) REVERT: B 522 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8619 (p) outliers start: 49 outliers final: 16 residues processed: 330 average time/residue: 0.3043 time to fit residues: 141.6584 Evaluate side-chains 312 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 592 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 0.0670 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14293 Z= 0.222 Angle : 0.635 12.045 19216 Z= 0.334 Chirality : 0.043 0.206 2108 Planarity : 0.004 0.065 2455 Dihedral : 7.052 86.964 1934 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.30 % Favored : 90.17 % Rotamer: Outliers : 3.67 % Allowed : 32.07 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1699 helix: 0.89 (0.20), residues: 737 sheet: -1.27 (0.39), residues: 184 loop : -3.22 (0.18), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 114 HIS 0.005 0.001 HIS B 676 PHE 0.016 0.002 PHE A 32 TYR 0.012 0.001 TYR A 373 ARG 0.004 0.000 ARG K 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 1.782 Fit side-chains REVERT: A 137 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 303 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 311 ASP cc_start: 0.7357 (t0) cc_final: 0.6941 (t70) REVERT: A 491 LYS cc_start: 0.8295 (tmtt) cc_final: 0.8047 (tttm) REVERT: B 368 GLU cc_start: 0.6923 (pm20) cc_final: 0.6209 (pm20) REVERT: B 385 ASP cc_start: 0.7526 (p0) cc_final: 0.7295 (p0) REVERT: B 522 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 613 ASP cc_start: 0.7116 (p0) cc_final: 0.6905 (p0) REVERT: B 641 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7588 (mppt) outliers start: 57 outliers final: 28 residues processed: 338 average time/residue: 0.3041 time to fit residues: 145.0822 Evaluate side-chains 327 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 592 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS K 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14293 Z= 0.371 Angle : 0.709 12.347 19216 Z= 0.374 Chirality : 0.047 0.199 2108 Planarity : 0.005 0.069 2455 Dihedral : 7.304 82.912 1934 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.89 % Favored : 89.58 % Rotamer: Outliers : 4.96 % Allowed : 30.59 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % 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: -1.83 (0.20), residues: 1699 helix: 0.72 (0.19), residues: 743 sheet: -1.38 (0.37), residues: 208 loop : -3.33 (0.18), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 157 HIS 0.007 0.002 HIS B 676 PHE 0.026 0.002 PHE A 32 TYR 0.019 0.002 TYR A 485 ARG 0.005 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 1.548 Fit side-chains REVERT: A 137 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6614 (t80) REVERT: A 303 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 311 ASP cc_start: 0.7418 (t0) cc_final: 0.7154 (t0) REVERT: A 443 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 491 LYS cc_start: 0.8289 (tmtt) cc_final: 0.8026 (tttm) REVERT: B 52 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: B 80 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: B 139 VAL cc_start: 0.8288 (m) cc_final: 0.8055 (p) REVERT: B 188 ASP cc_start: 0.7047 (p0) cc_final: 0.6824 (p0) REVERT: B 324 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 424 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 522 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8687 (p) REVERT: B 555 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 641 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7558 (mppt) REVERT: C 14 ASP cc_start: 0.8304 (p0) cc_final: 0.7945 (p0) outliers start: 77 outliers final: 49 residues processed: 367 average time/residue: 0.3021 time to fit residues: 156.2863 Evaluate side-chains 363 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 113 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 496 ASN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14293 Z= 0.209 Angle : 0.633 13.456 19216 Z= 0.329 Chirality : 0.043 0.207 2108 Planarity : 0.004 0.067 2455 Dihedral : 7.046 88.483 1934 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.01 % Favored : 90.46 % Rotamer: Outliers : 4.25 % Allowed : 31.81 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1699 helix: 0.97 (0.20), residues: 736 sheet: -1.03 (0.39), residues: 188 loop : -3.22 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 114 HIS 0.005 0.001 HIS B 676 PHE 0.015 0.001 PHE A 32 TYR 0.012 0.001 TYR A 134 ARG 0.002 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 306 time to evaluate : 1.684 Fit side-chains REVERT: A 137 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6416 (t80) REVERT: A 303 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 311 ASP cc_start: 0.7418 (t0) cc_final: 0.7211 (t0) REVERT: A 491 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7974 (tttm) REVERT: A 518 ASP cc_start: 0.7529 (m-30) cc_final: 0.7305 (m-30) REVERT: A 639 ARG cc_start: 0.7981 (tmm160) cc_final: 0.7758 (ttp80) REVERT: B 52 ASP cc_start: 0.8355 (t0) cc_final: 0.7929 (m-30) REVERT: B 188 ASP cc_start: 0.7029 (p0) cc_final: 0.6820 (p0) REVERT: B 324 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 364 ASP cc_start: 0.7834 (p0) cc_final: 0.7601 (p0) REVERT: B 368 GLU cc_start: 0.6962 (pm20) cc_final: 0.6310 (pm20) REVERT: B 385 ASP cc_start: 0.7463 (p0) cc_final: 0.7250 (p0) REVERT: B 424 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 555 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6438 (tm-30) REVERT: B 641 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7535 (mppt) REVERT: C 14 ASP cc_start: 0.8285 (p0) cc_final: 0.8079 (p0) REVERT: C 112 MET cc_start: 0.4377 (mtp) cc_final: 0.4156 (mtp) REVERT: K 689 MET cc_start: 0.5672 (ttm) cc_final: 0.5456 (ttp) outliers start: 66 outliers final: 45 residues processed: 350 average time/residue: 0.3024 time to fit residues: 149.3369 Evaluate side-chains 343 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 697 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 601 ASN B 461 GLN B 496 ASN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 253 ASN K 585 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14293 Z= 0.224 Angle : 0.634 13.833 19216 Z= 0.330 Chirality : 0.043 0.206 2108 Planarity : 0.004 0.065 2455 Dihedral : 6.981 88.934 1934 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.24 % Favored : 90.23 % Rotamer: Outliers : 5.02 % Allowed : 31.62 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1699 helix: 1.01 (0.20), residues: 737 sheet: -0.97 (0.39), residues: 190 loop : -3.18 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 114 HIS 0.006 0.001 HIS B 676 PHE 0.017 0.001 PHE A 32 TYR 0.013 0.001 TYR K 566 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 1.637 Fit side-chains REVERT: A 137 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6412 (t80) REVERT: A 303 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 328 GLU cc_start: 0.7306 (pt0) cc_final: 0.6983 (pt0) REVERT: A 443 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 491 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7969 (tttm) REVERT: A 518 ASP cc_start: 0.7487 (m-30) cc_final: 0.7243 (m-30) REVERT: A 576 GLU cc_start: 0.7317 (mp0) cc_final: 0.7010 (mp0) REVERT: B 52 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: B 219 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7324 (mmmt) REVERT: B 324 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 364 ASP cc_start: 0.7815 (p0) cc_final: 0.7586 (p0) REVERT: B 368 GLU cc_start: 0.6952 (pm20) cc_final: 0.6413 (pm20) REVERT: B 370 ILE cc_start: 0.8271 (pt) cc_final: 0.7968 (tt) REVERT: B 424 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 522 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 555 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6417 (tm-30) REVERT: B 641 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7494 (mppt) REVERT: C 14 ASP cc_start: 0.8303 (p0) cc_final: 0.7981 (p0) REVERT: C 112 MET cc_start: 0.4323 (mtp) cc_final: 0.4113 (mtp) outliers start: 78 outliers final: 54 residues processed: 364 average time/residue: 0.2994 time to fit residues: 154.3927 Evaluate side-chains 357 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 697 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 375 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14293 Z= 0.209 Angle : 0.641 14.485 19216 Z= 0.330 Chirality : 0.043 0.193 2108 Planarity : 0.004 0.065 2455 Dihedral : 6.910 86.753 1934 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.06 % Favored : 90.41 % Rotamer: Outliers : 5.09 % Allowed : 32.07 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1699 helix: 1.09 (0.20), residues: 737 sheet: -0.88 (0.39), residues: 188 loop : -3.15 (0.18), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 114 HIS 0.004 0.001 HIS A 676 PHE 0.015 0.001 PHE A 32 TYR 0.013 0.001 TYR A 216 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 1.580 Fit side-chains REVERT: A 137 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6375 (t80) REVERT: A 303 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 311 ASP cc_start: 0.7162 (t0) cc_final: 0.6899 (t70) REVERT: A 328 GLU cc_start: 0.7320 (pt0) cc_final: 0.7010 (pt0) REVERT: A 443 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 491 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7965 (tttm) REVERT: A 518 ASP cc_start: 0.7333 (m-30) cc_final: 0.7079 (m-30) REVERT: A 576 GLU cc_start: 0.7282 (mp0) cc_final: 0.7005 (mp0) REVERT: A 606 MET cc_start: 0.8530 (mmt) cc_final: 0.8294 (mmt) REVERT: A 639 ARG cc_start: 0.7964 (tmm160) cc_final: 0.7730 (ttp80) REVERT: B 52 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: B 324 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 364 ASP cc_start: 0.7773 (p0) cc_final: 0.7536 (p0) REVERT: B 368 GLU cc_start: 0.6948 (pm20) cc_final: 0.6340 (pm20) REVERT: B 370 ILE cc_start: 0.8265 (pt) cc_final: 0.7977 (tt) REVERT: B 424 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 522 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8664 (p) REVERT: B 555 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6386 (tm-30) REVERT: B 613 ASP cc_start: 0.7015 (p0) cc_final: 0.6568 (p0) REVERT: B 641 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7518 (mppt) REVERT: C 14 ASP cc_start: 0.8306 (p0) cc_final: 0.8025 (p0) REVERT: K 586 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5505 (tt0) outliers start: 79 outliers final: 61 residues processed: 362 average time/residue: 0.2957 time to fit residues: 150.4111 Evaluate side-chains 366 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 298 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 544 ILE Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 586 GLU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14293 Z= 0.194 Angle : 0.637 14.979 19216 Z= 0.329 Chirality : 0.042 0.219 2108 Planarity : 0.004 0.063 2455 Dihedral : 6.831 85.269 1934 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.12 % Favored : 90.41 % Rotamer: Outliers : 5.02 % Allowed : 32.52 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1699 helix: 1.12 (0.20), residues: 740 sheet: -0.89 (0.39), residues: 190 loop : -3.08 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 114 HIS 0.004 0.001 HIS B 676 PHE 0.014 0.001 PHE A 32 TYR 0.011 0.001 TYR A 373 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 1.521 Fit side-chains REVERT: A 137 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6362 (t80) REVERT: A 303 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 311 ASP cc_start: 0.7230 (t0) cc_final: 0.6981 (t70) REVERT: A 328 GLU cc_start: 0.7320 (pt0) cc_final: 0.7013 (pt0) REVERT: A 443 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 491 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7957 (tttm) REVERT: A 574 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6931 (mtmt) REVERT: A 576 GLU cc_start: 0.7251 (mp0) cc_final: 0.7000 (mp0) REVERT: A 639 ARG cc_start: 0.7941 (tmm160) cc_final: 0.7702 (ttp80) REVERT: B 52 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: B 324 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 326 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: B 364 ASP cc_start: 0.7755 (p0) cc_final: 0.7510 (p0) REVERT: B 368 GLU cc_start: 0.6936 (pm20) cc_final: 0.6383 (pm20) REVERT: B 370 ILE cc_start: 0.8286 (pt) cc_final: 0.7983 (tt) REVERT: B 424 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7095 (mm-30) REVERT: B 451 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 522 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 555 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6362 (tm-30) REVERT: B 613 ASP cc_start: 0.6998 (p0) cc_final: 0.6584 (p0) REVERT: B 641 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7541 (mppt) REVERT: C 14 ASP cc_start: 0.8276 (p0) cc_final: 0.8036 (p0) REVERT: K 586 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5502 (tt0) outliers start: 78 outliers final: 61 residues processed: 354 average time/residue: 0.3018 time to fit residues: 149.8251 Evaluate side-chains 360 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 544 ILE Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 586 GLU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 0.0020 chunk 91 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 496 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14293 Z= 0.182 Angle : 0.643 16.341 19216 Z= 0.328 Chirality : 0.042 0.225 2108 Planarity : 0.004 0.059 2455 Dihedral : 6.743 83.116 1934 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.12 % Favored : 90.52 % Rotamer: Outliers : 4.57 % Allowed : 32.58 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1699 helix: 1.17 (0.20), residues: 739 sheet: -0.77 (0.40), residues: 188 loop : -3.06 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 114 HIS 0.004 0.001 HIS A 676 PHE 0.012 0.001 PHE A 32 TYR 0.011 0.001 TYR A 373 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 1.661 Fit side-chains REVERT: A 137 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 303 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 311 ASP cc_start: 0.7244 (t0) cc_final: 0.6965 (t70) REVERT: A 328 GLU cc_start: 0.7326 (pt0) cc_final: 0.7009 (pt0) REVERT: A 443 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 491 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7964 (tttm) REVERT: A 518 ASP cc_start: 0.7279 (m-30) cc_final: 0.7012 (m-30) REVERT: A 576 GLU cc_start: 0.7224 (mp0) cc_final: 0.6988 (mp0) REVERT: A 606 MET cc_start: 0.8543 (mmt) cc_final: 0.8327 (mmt) REVERT: A 639 ARG cc_start: 0.7945 (tmm160) cc_final: 0.7716 (ttp80) REVERT: B 52 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: B 324 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 326 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: B 364 ASP cc_start: 0.7717 (p0) cc_final: 0.7484 (p0) REVERT: B 368 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: B 370 ILE cc_start: 0.8291 (pt) cc_final: 0.7998 (tt) REVERT: B 424 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7082 (mm-30) REVERT: B 451 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 555 GLU cc_start: 0.6695 (tm-30) cc_final: 0.6318 (tm-30) REVERT: B 613 ASP cc_start: 0.6976 (p0) cc_final: 0.6574 (p0) REVERT: B 641 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7541 (mppt) REVERT: C 14 ASP cc_start: 0.8263 (p0) cc_final: 0.8029 (p0) REVERT: K 586 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5508 (tt0) outliers start: 71 outliers final: 57 residues processed: 344 average time/residue: 0.3101 time to fit residues: 149.9164 Evaluate side-chains 357 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 544 ILE Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 586 GLU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 50.0000 chunk 14 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 101 ASN B 496 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14293 Z= 0.228 Angle : 0.664 14.447 19216 Z= 0.342 Chirality : 0.043 0.228 2108 Planarity : 0.004 0.061 2455 Dihedral : 6.865 87.488 1934 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.77 % Favored : 89.82 % Rotamer: Outliers : 4.57 % Allowed : 32.71 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1699 helix: 1.17 (0.20), residues: 737 sheet: -0.99 (0.39), residues: 197 loop : -3.03 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 114 HIS 0.005 0.001 HIS B 676 PHE 0.017 0.001 PHE A 32 TYR 0.012 0.001 TYR C 155 ARG 0.004 0.000 ARG B 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 1.650 Fit side-chains REVERT: A 137 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6334 (t80) REVERT: A 303 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 311 ASP cc_start: 0.7253 (t0) cc_final: 0.6982 (t70) REVERT: A 328 GLU cc_start: 0.7322 (pt0) cc_final: 0.7009 (pt0) REVERT: A 443 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 491 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: A 518 ASP cc_start: 0.7451 (m-30) cc_final: 0.7175 (m-30) REVERT: A 576 GLU cc_start: 0.7282 (mp0) cc_final: 0.7075 (mp0) REVERT: A 639 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7728 (ttp80) REVERT: B 52 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: B 139 VAL cc_start: 0.8152 (p) cc_final: 0.7857 (m) REVERT: B 324 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 326 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: B 364 ASP cc_start: 0.7700 (p0) cc_final: 0.7471 (p0) REVERT: B 368 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: B 370 ILE cc_start: 0.8299 (pt) cc_final: 0.8019 (tt) REVERT: B 424 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 451 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 522 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8660 (p) REVERT: B 555 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6337 (tm-30) REVERT: B 613 ASP cc_start: 0.6958 (p0) cc_final: 0.6582 (p0) REVERT: B 641 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7513 (mppt) REVERT: K 586 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5510 (tt0) outliers start: 71 outliers final: 58 residues processed: 351 average time/residue: 0.3095 time to fit residues: 151.6028 Evaluate side-chains 365 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 544 ILE Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 586 GLU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN B 101 ASN B 496 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118608 restraints weight = 20005.287| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.50 r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 14293 Z= 0.268 Angle : 1.030 59.200 19216 Z= 0.596 Chirality : 0.046 0.585 2108 Planarity : 0.005 0.078 2455 Dihedral : 6.975 87.498 1934 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.12 % Favored : 89.52 % Rotamer: Outliers : 4.51 % Allowed : 32.84 % Favored : 62.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.12 % 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: -1.31 (0.20), residues: 1699 helix: 1.14 (0.20), residues: 737 sheet: -0.99 (0.39), residues: 197 loop : -3.03 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 114 HIS 0.012 0.001 HIS B 676 PHE 0.018 0.001 PHE A 32 TYR 0.011 0.001 TYR B 472 ARG 0.004 0.000 ARG B 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.26 seconds wall clock time: 66 minutes 24.44 seconds (3984.44 seconds total)