Starting phenix.real_space_refine on Fri Jul 3 12:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr0_14875/07_2026/7zr0_14875.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.21, per 1000 atoms: 0.23 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: 0.99 Conformation dependent library (CDL) restraints added in 647.9 milliseconds 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: 0.34 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: 2.38 Time building geometry restraints manager: 1.40 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: 7133 17.95 - 35.90: 1252 35.90 - 53.85: 340 53.85 - 71.80: 64 71.80 - 89.74: 28 Dihedral angle restraints: 8817 sinusoidal: 3764 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 8814 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 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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= 0.245 Angle : 0.995 73.851 19216 Z= 0.497 Chirality : 0.046 0.216 2108 Planarity : 0.006 0.118 2455 Dihedral : 19.798 89.744 5533 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.46 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (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 ARG 0.010 0.000 ARG C 167 TYR 0.026 0.002 TYR A 137 PHE 0.023 0.002 PHE B 165 TRP 0.021 0.002 TRP C 114 HIS 0.009 0.002 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.25 (14293) covalent geometry : angle 0.99511 / 0.50 (19216) hydrogen bonds : bond 0.19768 / 12.30 ( 550) hydrogen bonds : angle 6.32932 / 4.34 ( 1614) *********************** 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 : 0.545 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: 0.1415 time to fit residues: 59.2909 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 : 0.579 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0030 chunk 149 optimal weight: 9.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119786 restraints weight = 20357.023| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.27 r_work: 0.3334 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14293 Z= 0.152 Angle : 0.663 12.370 19216 Z= 0.351 Chirality : 0.043 0.208 2108 Planarity : 0.005 0.078 2455 Dihedral : 5.582 53.828 1874 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.89 % Favored : 90.64 % Rotamer: Outliers : 3.09 % Allowed : 32.52 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.20), residues: 1699 helix: 0.80 (0.20), residues: 727 sheet: -1.73 (0.39), residues: 185 loop : -3.26 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 575 TYR 0.013 0.001 TYR A 137 PHE 0.013 0.002 PHE B 165 TRP 0.023 0.002 TRP C 114 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14293) covalent geometry : angle 0.66253 / 0.35 (19216) hydrogen bonds : bond 0.05640 / 3.63 ( 550) hydrogen bonds : angle 4.93641 / 3.44 ( 1614) *********************** 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 353 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 0.620 Fit side-chains REVERT: A 137 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5971 (t80) REVERT: A 303 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: A 311 ASP cc_start: 0.7582 (t0) cc_final: 0.7259 (t70) REVERT: A 380 VAL cc_start: 0.8593 (m) cc_final: 0.8378 (t) REVERT: A 491 LYS cc_start: 0.8354 (tmtt) cc_final: 0.8065 (tttm) REVERT: B 277 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7569 (pt) REVERT: B 454 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 522 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8546 (p) outliers start: 48 outliers final: 20 residues processed: 332 average time/residue: 0.1321 time to fit residues: 62.4041 Evaluate side-chains 319 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 294 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 461 GLN 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 277 ILE Chi-restraints excluded: chain B residue 454 LEU 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 579 THR Chi-restraints excluded: chain B residue 581 SER 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 19 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS ** K 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122616 restraints weight = 20323.280| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.20 r_work: 0.3357 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14293 Z= 0.135 Angle : 0.623 12.180 19216 Z= 0.326 Chirality : 0.043 0.203 2108 Planarity : 0.004 0.064 2455 Dihedral : 5.348 52.518 1872 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.77 % Favored : 90.70 % Rotamer: Outliers : 3.86 % Allowed : 32.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1699 helix: 0.95 (0.20), residues: 730 sheet: -1.17 (0.40), residues: 178 loop : -3.20 (0.18), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 475 TYR 0.012 0.001 TYR C 155 PHE 0.014 0.001 PHE A 32 TRP 0.020 0.002 TRP C 114 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14293) covalent geometry : angle 0.62295 / 0.33 (19216) hydrogen bonds : bond 0.05124 / 3.28 ( 550) hydrogen bonds : angle 4.73928 / 3.32 ( 1614) *********************** 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: 60 poor density : 301 time to evaluate : 0.521 Fit side-chains REVERT: A 137 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.5948 (t80) REVERT: A 303 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 311 ASP cc_start: 0.7595 (t0) cc_final: 0.7183 (t70) REVERT: A 380 VAL cc_start: 0.8615 (m) cc_final: 0.8407 (t) REVERT: A 491 LYS cc_start: 0.8301 (tmtt) cc_final: 0.8062 (tttm) REVERT: B 86 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 277 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7514 (pt) REVERT: B 324 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 368 GLU cc_start: 0.7189 (pm20) cc_final: 0.6460 (pm20) REVERT: B 454 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8277 (mt) REVERT: B 522 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 613 ASP cc_start: 0.7443 (p0) cc_final: 0.7198 (p0) REVERT: B 641 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7655 (mppt) REVERT: K 618 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6503 (mt) outliers start: 60 outliers final: 25 residues processed: 338 average time/residue: 0.1359 time to fit residues: 65.0416 Evaluate side-chains 323 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 B residue 32 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 468 SER 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 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 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 Chi-restraints excluded: chain K residue 618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 86 optimal weight: 0.0270 chunk 98 optimal weight: 0.0980 chunk 15 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 154 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN B 609 GLN ** K 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126744 restraints weight = 20542.223| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.21 r_work: 0.3429 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 14293 Z= 0.109 Angle : 0.575 12.824 19216 Z= 0.300 Chirality : 0.041 0.199 2108 Planarity : 0.004 0.054 2455 Dihedral : 4.948 48.249 1872 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.06 % Favored : 91.47 % Rotamer: Outliers : 3.41 % Allowed : 32.26 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1699 helix: 1.18 (0.20), residues: 726 sheet: -0.97 (0.41), residues: 173 loop : -3.05 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.012 0.001 TYR C 155 PHE 0.009 0.001 PHE A 39 TRP 0.019 0.001 TRP C 114 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14293) covalent geometry : angle 0.57516 / 0.30 (19216) hydrogen bonds : bond 0.03950 / 2.50 ( 550) hydrogen bonds : angle 4.50401 / 3.17 ( 1614) *********************** 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 358 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.535 Fit side-chains REVERT: A 137 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5887 (t80) REVERT: A 491 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7941 (tttm) REVERT: B 52 ASP cc_start: 0.8317 (t0) cc_final: 0.7864 (m-30) REVERT: B 277 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7414 (pt) REVERT: B 368 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: B 555 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6521 (tm-30) REVERT: B 641 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7688 (mppt) outliers start: 53 outliers final: 30 residues processed: 339 average time/residue: 0.1323 time to fit residues: 64.0685 Evaluate side-chains 319 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 391 SER 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 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 23 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS 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 524 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 130 ASN C 253 ASN K 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118911 restraints weight = 20299.231| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.34 r_work: 0.3292 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14293 Z= 0.231 Angle : 0.694 13.523 19216 Z= 0.363 Chirality : 0.046 0.204 2108 Planarity : 0.005 0.061 2455 Dihedral : 5.256 52.193 1870 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.54 % Favored : 89.94 % Rotamer: Outliers : 4.70 % Allowed : 31.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1699 helix: 0.93 (0.20), residues: 738 sheet: -1.19 (0.37), residues: 205 loop : -3.14 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 359 TYR 0.021 0.002 TYR A 134 PHE 0.023 0.002 PHE A 32 TRP 0.017 0.002 TRP B 157 HIS 0.006 0.001 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (14293) covalent geometry : angle 0.69433 / 0.36 (19216) hydrogen bonds : bond 0.06215 / 4.04 ( 550) hydrogen bonds : angle 4.72973 / 3.32 ( 1614) *********************** 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 385 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 312 time to evaluate : 0.531 Fit side-chains REVERT: A 137 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6081 (t80) REVERT: A 303 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 443 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 491 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7951 (tttm) REVERT: B 52 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: B 80 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: B 81 GLU cc_start: 0.7291 (mp0) cc_final: 0.7077 (mp0) REVERT: B 188 ASP cc_start: 0.7143 (p0) cc_final: 0.6901 (p0) REVERT: B 277 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7447 (pt) REVERT: B 359 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.8069 (mtm-85) REVERT: B 424 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: B 461 GLN cc_start: 0.7796 (mt0) cc_final: 0.7587 (mt0) REVERT: B 522 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 555 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6626 (tm-30) REVERT: B 641 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7508 (mppt) REVERT: C 14 ASP cc_start: 0.8307 (p0) cc_final: 0.8099 (p0) REVERT: K 650 MET cc_start: 0.7840 (mtp) cc_final: 0.7481 (mtt) outliers start: 73 outliers final: 49 residues processed: 362 average time/residue: 0.1341 time to fit residues: 68.7435 Evaluate side-chains 357 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 385 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR 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 B residue 29 ILE 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 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 277 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 424 GLU 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 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 595 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 40.0000 chunk 113 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN A 601 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN K 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120883 restraints weight = 20302.958| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.38 r_work: 0.3312 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1845 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= 0.143 Angle : 0.633 14.110 19216 Z= 0.328 Chirality : 0.043 0.194 2108 Planarity : 0.004 0.060 2455 Dihedral : 5.121 52.227 1870 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.06 % Favored : 90.46 % Rotamer: Outliers : 4.51 % Allowed : 32.07 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1699 helix: 1.03 (0.20), residues: 743 sheet: -0.94 (0.39), residues: 190 loop : -3.13 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 359 TYR 0.017 0.001 TYR A 134 PHE 0.015 0.001 PHE A 32 TRP 0.019 0.001 TRP C 114 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14293) covalent geometry : angle 0.63262 / 0.33 (19216) hydrogen bonds : bond 0.04951 / 3.19 ( 550) hydrogen bonds : angle 4.61740 / 3.26 ( 1614) *********************** 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 381 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 0.547 Fit side-chains REVERT: A 137 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5928 (t80) REVERT: A 303 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 328 GLU cc_start: 0.7791 (pt0) cc_final: 0.7373 (pt0) REVERT: A 443 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 491 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7969 (tttm) REVERT: A 574 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6912 (mtmt) REVERT: B 52 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: B 80 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: B 81 GLU cc_start: 0.7071 (mp0) cc_final: 0.6839 (mp0) REVERT: B 188 ASP cc_start: 0.7156 (p0) cc_final: 0.6909 (p0) REVERT: B 219 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7316 (mmmt) REVERT: B 277 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7441 (pt) REVERT: B 368 GLU cc_start: 0.7181 (pm20) cc_final: 0.6419 (pm20) REVERT: B 385 ASP cc_start: 0.7796 (p0) cc_final: 0.7511 (p0) REVERT: B 555 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6468 (tm-30) REVERT: B 641 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7482 (mppt) REVERT: C 14 ASP cc_start: 0.8298 (p0) cc_final: 0.8093 (p0) REVERT: K 650 MET cc_start: 0.7864 (mtp) cc_final: 0.7405 (mtt) outliers start: 70 outliers final: 48 residues processed: 358 average time/residue: 0.1320 time to fit residues: 67.1077 Evaluate side-chains 356 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 481 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 B residue 32 PHE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 80 GLN 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 277 ILE Chi-restraints excluded: chain B residue 468 SER 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 130 ASN 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 595 PHE Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 92 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 119 optimal weight: 1.9990 chunk 137 optimal weight: 0.0370 overall best weight: 0.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN A 375 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN K 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121084 restraints weight = 20219.530| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.64 r_work: 0.3336 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14293 Z= 0.116 Angle : 0.609 13.622 19216 Z= 0.314 Chirality : 0.041 0.188 2108 Planarity : 0.004 0.057 2455 Dihedral : 4.852 49.409 1870 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.89 % Favored : 90.64 % Rotamer: Outliers : 4.25 % Allowed : 33.10 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1699 helix: 1.26 (0.20), residues: 731 sheet: -0.80 (0.39), residues: 191 loop : -3.02 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.013 0.001 TYR A 134 PHE 0.009 0.001 PHE A 39 TRP 0.021 0.001 TRP C 114 HIS 0.005 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14293) covalent geometry : angle 0.60918 / 0.31 (19216) hydrogen bonds : bond 0.04122 / 2.64 ( 550) hydrogen bonds : angle 4.49935 / 3.18 ( 1614) *********************** 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 366 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 300 time to evaluate : 0.518 Fit side-chains REVERT: A 125 MET cc_start: 0.7669 (mtp) cc_final: 0.7405 (mtt) REVERT: A 137 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5858 (t80) REVERT: A 303 GLU cc_start: 0.7494 (tp30) cc_final: 0.7136 (mp0) REVERT: A 491 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7836 (tttm) REVERT: B 52 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 80 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: B 81 GLU cc_start: 0.6784 (mp0) cc_final: 0.6557 (mp0) REVERT: B 114 MET cc_start: 0.7587 (tpp) cc_final: 0.7200 (tpp) REVERT: B 368 GLU cc_start: 0.6967 (pm20) cc_final: 0.6298 (pm20) REVERT: B 385 ASP cc_start: 0.7498 (p0) cc_final: 0.7237 (p0) REVERT: B 555 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6220 (tm-30) REVERT: B 641 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7408 (mppt) REVERT: C 14 ASP cc_start: 0.8116 (p0) cc_final: 0.7868 (p0) REVERT: C 112 MET cc_start: 0.4154 (mtp) cc_final: 0.3935 (mtp) REVERT: K 650 MET cc_start: 0.7523 (mtp) cc_final: 0.7182 (mtt) outliers start: 66 outliers final: 50 residues processed: 346 average time/residue: 0.1383 time to fit residues: 67.9022 Evaluate side-chains 345 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 391 SER 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 494 VAL 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 A residue 671 GLU Chi-restraints excluded: chain B residue 32 PHE 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 468 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 564 CYS 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 41 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 ASN 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 648 GLU Chi-restraints excluded: chain K residue 668 MET 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 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 63 optimal weight: 0.0570 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119372 restraints weight = 20229.521| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.53 r_work: 0.3308 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14293 Z= 0.155 Angle : 0.649 14.828 19216 Z= 0.335 Chirality : 0.043 0.221 2108 Planarity : 0.004 0.058 2455 Dihedral : 4.966 50.187 1870 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.42 % Favored : 90.17 % Rotamer: Outliers : 4.44 % Allowed : 32.84 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1699 helix: 1.16 (0.20), residues: 737 sheet: -0.69 (0.40), residues: 187 loop : -2.99 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.020 0.001 TYR A 134 PHE 0.017 0.002 PHE A 32 TRP 0.017 0.002 TRP C 114 HIS 0.005 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14293) covalent geometry : angle 0.64861 / 0.34 (19216) hydrogen bonds : bond 0.05087 / 3.29 ( 550) hydrogen bonds : angle 4.56656 / 3.22 ( 1614) *********************** 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 372 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.476 Fit side-chains REVERT: A 137 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.5741 (t80) REVERT: A 303 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 328 GLU cc_start: 0.7474 (pt0) cc_final: 0.7089 (pt0) REVERT: A 443 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 491 LYS cc_start: 0.8074 (tmtt) cc_final: 0.7867 (tttm) REVERT: A 518 ASP cc_start: 0.7293 (m-30) cc_final: 0.6978 (m-30) REVERT: A 639 ARG cc_start: 0.7975 (tmm160) cc_final: 0.7767 (ttp80) REVERT: B 52 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: B 80 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: B 81 GLU cc_start: 0.6974 (mp0) cc_final: 0.6771 (mp0) REVERT: B 139 VAL cc_start: 0.7898 (p) cc_final: 0.7549 (m) REVERT: B 368 GLU cc_start: 0.6956 (pm20) cc_final: 0.6330 (pm20) REVERT: B 555 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6305 (tm-30) REVERT: B 641 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7362 (mppt) REVERT: C 14 ASP cc_start: 0.8170 (p0) cc_final: 0.7947 (p0) REVERT: C 112 MET cc_start: 0.4230 (mtp) cc_final: 0.4018 (mtp) REVERT: K 650 MET cc_start: 0.7644 (mtp) cc_final: 0.7307 (mtt) outliers start: 69 outliers final: 49 residues processed: 352 average time/residue: 0.1367 time to fit residues: 68.3800 Evaluate side-chains 348 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 446 THR 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 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 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 468 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 543 LEU 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 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 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 668 MET 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 67 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 601 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 146 GLN K 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118802 restraints weight = 20320.270| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.53 r_work: 0.3298 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14293 Z= 0.167 Angle : 0.665 14.483 19216 Z= 0.344 Chirality : 0.044 0.229 2108 Planarity : 0.004 0.060 2455 Dihedral : 5.096 51.988 1870 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.36 % Favored : 90.23 % Rotamer: Outliers : 4.19 % Allowed : 32.78 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.20), residues: 1699 helix: 1.14 (0.20), residues: 737 sheet: -0.95 (0.39), residues: 196 loop : -2.99 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 359 TYR 0.022 0.002 TYR A 134 PHE 0.018 0.002 PHE A 32 TRP 0.016 0.002 TRP C 114 HIS 0.005 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14293) covalent geometry : angle 0.66497 / 0.34 (19216) hydrogen bonds : bond 0.05217 / 3.37 ( 550) hydrogen bonds : angle 4.60559 / 3.25 ( 1614) *********************** 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 366 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 0.540 Fit side-chains REVERT: A 137 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.5712 (t80) REVERT: A 200 GLU cc_start: 0.7363 (tt0) cc_final: 0.7000 (pt0) REVERT: A 303 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 328 GLU cc_start: 0.7466 (pt0) cc_final: 0.7081 (pt0) REVERT: A 443 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 491 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7882 (tttm) REVERT: A 518 ASP cc_start: 0.7348 (m-30) cc_final: 0.7024 (m-30) REVERT: A 639 ARG cc_start: 0.7972 (tmm160) cc_final: 0.7762 (ttp80) REVERT: B 52 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: B 80 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: B 139 VAL cc_start: 0.7915 (p) cc_final: 0.7522 (m) REVERT: B 368 GLU cc_start: 0.6961 (pm20) cc_final: 0.6339 (pm20) REVERT: B 370 ILE cc_start: 0.8317 (pt) cc_final: 0.8002 (tt) REVERT: B 385 ASP cc_start: 0.7527 (p0) cc_final: 0.7294 (p0) REVERT: B 522 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 555 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6340 (tm-30) REVERT: B 641 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7411 (mppt) REVERT: C 14 ASP cc_start: 0.8172 (p0) cc_final: 0.7845 (p0) REVERT: C 112 MET cc_start: 0.4332 (mtp) cc_final: 0.4098 (mtp) REVERT: K 650 MET cc_start: 0.7719 (mtp) cc_final: 0.7396 (mtt) outliers start: 65 outliers final: 50 residues processed: 345 average time/residue: 0.1214 time to fit residues: 59.5970 Evaluate side-chains 355 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 187 GLU 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 391 SER 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 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 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 468 SER Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 543 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 146 GLN K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119004 restraints weight = 20239.264| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.52 r_work: 0.3299 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14293 Z= 0.161 Angle : 0.672 15.482 19216 Z= 0.345 Chirality : 0.044 0.235 2108 Planarity : 0.004 0.062 2455 Dihedral : 5.104 52.538 1870 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.59 % Favored : 89.99 % Rotamer: Outliers : 4.06 % Allowed : 33.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.20), residues: 1699 helix: 1.14 (0.20), residues: 737 sheet: -1.01 (0.39), residues: 197 loop : -2.99 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.020 0.001 TYR A 134 PHE 0.017 0.002 PHE A 32 TRP 0.017 0.001 TRP C 114 HIS 0.005 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (14293) covalent geometry : angle 0.67250 / 0.35 (19216) hydrogen bonds : bond 0.05087 / 3.29 ( 550) hydrogen bonds : angle 4.58536 / 3.23 ( 1614) ********************** 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 364 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 301 time to evaluate : 0.445 Fit side-chains REVERT: A 137 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 200 GLU cc_start: 0.7675 (tt0) cc_final: 0.7234 (pt0) REVERT: A 303 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 328 GLU cc_start: 0.7817 (pt0) cc_final: 0.7421 (pt0) REVERT: A 443 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 491 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7949 (tttm) REVERT: A 518 ASP cc_start: 0.7513 (m-30) cc_final: 0.7201 (m-30) REVERT: B 52 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 139 VAL cc_start: 0.7981 (p) cc_final: 0.7566 (m) REVERT: B 368 GLU cc_start: 0.7118 (pm20) cc_final: 0.6450 (pm20) REVERT: B 370 ILE cc_start: 0.8317 (pt) cc_final: 0.8013 (tt) REVERT: B 385 ASP cc_start: 0.7761 (p0) cc_final: 0.7509 (p0) REVERT: B 522 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 555 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6467 (tm-30) REVERT: B 562 ASN cc_start: 0.8371 (t0) cc_final: 0.8165 (t0) REVERT: B 641 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7513 (mppt) REVERT: C 14 ASP cc_start: 0.8282 (p0) cc_final: 0.8015 (p0) REVERT: C 112 MET cc_start: 0.4963 (mtp) cc_final: 0.4678 (mtp) REVERT: K 650 MET cc_start: 0.7995 (mtp) cc_final: 0.7627 (mtt) outliers start: 63 outliers final: 50 residues processed: 346 average time/residue: 0.1331 time to fit residues: 64.9111 Evaluate side-chains 352 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 187 GLU 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 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 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 57 GLU 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 468 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 543 LEU 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 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.0170 chunk 28 optimal weight: 0.1980 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN 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 = 0.3910 r_free = 0.3910 target = 0.153428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119558 restraints weight = 20189.450| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.64 r_work: 0.3299 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14293 Z= 0.134 Angle : 0.656 14.790 19216 Z= 0.337 Chirality : 0.043 0.367 2108 Planarity : 0.004 0.064 2455 Dihedral : 5.038 52.150 1870 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.36 % Favored : 90.29 % Rotamer: Outliers : 3.41 % Allowed : 33.93 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.20), residues: 1699 helix: 1.16 (0.20), residues: 746 sheet: -0.76 (0.40), residues: 188 loop : -3.08 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.019 0.001 TYR A 134 PHE 0.013 0.001 PHE A 32 TRP 0.019 0.001 TRP C 114 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14293) covalent geometry : angle 0.65596 / 0.34 (19216) hydrogen bonds : bond 0.04691 / 3.03 ( 550) hydrogen bonds : angle 4.55162 / 3.21 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3729.70 seconds wall clock time: 64 minutes 41.47 seconds (3881.47 seconds total)