Starting phenix.real_space_refine on Sun Aug 24 16:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yif_33857/08_2025/7yif_33857.map" } resolution = 3.5 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= 0.054 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 K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21322 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.20 Number of scatterers: 21322 At special positions: 0 Unit cell: (160.461, 160.461, 130.746, 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) K 6 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 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: 1.57 Conformation dependent library (CDL) restraints added in 899.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 24 sheets defined 52.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET A 68 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.612A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 416 through 431 removed outlier: 4.112A pdb=" N VAL A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.936A pdb=" N ARG A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG A 552 " --> pdb=" O PRO A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 643 through 651 Processing helix chain 'A' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET B 68 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 345 through 374 removed outlier: 3.612A pdb=" N LEU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.922A pdb=" N ARG B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 546' Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG B 552 " --> pdb=" O PRO B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET C 68 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 345 through 374 removed outlier: 3.611A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.922A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 546' Processing helix chain 'C' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG C 552 " --> pdb=" O PRO C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 692 Processing helix chain 'D' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET D 68 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS D 148 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 345 through 374 removed outlier: 3.611A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 395 Processing helix chain 'D' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 454 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.908A pdb=" N ARG D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 546' Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG D 552 " --> pdb=" O PRO D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL A 584 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA A 624 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AB1, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL B 584 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA B 624 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AB7, first strand: chain 'C' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL C 584 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA C 624 " --> pdb=" O VAL C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 94 through 97 Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AC4, first strand: chain 'D' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL D 584 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA D 624 " --> pdb=" O VAL D 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 920 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6700 1.34 - 1.46: 4763 1.46 - 1.58: 10149 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CA ILE B 191 " pdb=" CB ILE B 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE D 191 " pdb=" CB ILE D 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE C 191 " pdb=" CB ILE C 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE A 191 " pdb=" CB ILE A 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CG ARG D 21 " pdb=" CD ARG D 21 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.46e-01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 28988 1.69 - 3.37: 504 3.37 - 5.06: 68 5.06 - 6.75: 8 6.75 - 8.44: 16 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" C ASP A 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP D 57 " pdb=" CA ASP D 57 " pdb=" C ASP D 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP B 57 " pdb=" CA ASP B 57 " pdb=" C ASP B 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP C 57 " pdb=" CA ASP C 57 " pdb=" C ASP C 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" C THR C 441 " pdb=" N THR C 442 " pdb=" CA THR C 442 " ideal model delta sigma weight residual 121.54 114.78 6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 11429 16.44 - 32.87: 1182 32.87 - 49.31: 265 49.31 - 65.74: 40 65.74 - 82.18: 16 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR C 291 " pdb=" C THR C 291 " pdb=" N TRP C 292 " pdb=" CA TRP C 292 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA THR A 291 " pdb=" C THR A 291 " pdb=" N TRP A 292 " pdb=" CA TRP A 292 " ideal model delta harmonic sigma weight residual 180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA THR D 291 " pdb=" C THR D 291 " pdb=" N TRP D 292 " pdb=" CA TRP D 292 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1943 0.028 - 0.055: 965 0.055 - 0.083: 338 0.083 - 0.110: 118 0.110 - 0.138: 40 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA THR A 441 " pdb=" N THR A 441 " pdb=" C THR A 441 " pdb=" CB THR A 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR C 441 " pdb=" N THR C 441 " pdb=" C THR C 441 " pdb=" CB THR C 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR D 441 " pdb=" N THR D 441 " pdb=" C THR D 441 " pdb=" CB THR D 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 104 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 103 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 104 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 103 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO D 104 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.023 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 6694 2.84 - 3.41: 22290 3.41 - 3.99: 36904 3.99 - 4.56: 52089 4.56 - 5.14: 79465 Nonbonded interactions: 197442 Sorted by model distance: nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR D 195 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR A 195 " pdb=" OE2 GLU B 596 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 195 " pdb=" OE2 GLU D 596 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 195 " pdb=" OE2 GLU C 596 " model vdw 2.259 3.040 nonbonded pdb=" O LEU D 418 " pdb=" OG SER D 422 " model vdw 2.280 3.040 ... (remaining 197437 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 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.050 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.002 0.026 21804 Z= 0.113 Angle : 0.576 8.436 29584 Z= 0.328 Chirality : 0.039 0.138 3404 Planarity : 0.004 0.042 3668 Dihedral : 14.019 82.179 7884 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.49 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 aren not related in a simple way. whole: -1.85 (0.16), residues: 2616 helix: 0.28 (0.15), residues: 1256 sheet: -3.62 (0.37), residues: 188 loop : -2.55 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.011 0.001 TYR A 460 PHE 0.016 0.001 PHE D 226 TRP 0.013 0.001 TRP D 217 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00220 (21804) covalent geometry : angle 0.57616 (29584) hydrogen bonds : bond 0.18382 ( 920) hydrogen bonds : angle 5.89250 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.0244 (ppp) cc_final: -0.0988 (ppp) REVERT: A 290 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7071 (tptt) REVERT: B 169 MET cc_start: 0.0246 (ppp) cc_final: -0.0993 (ppp) REVERT: B 290 LYS cc_start: 0.7430 (ttmm) cc_final: 0.7068 (tptt) REVERT: C 169 MET cc_start: 0.0245 (ppp) cc_final: -0.0997 (ppp) REVERT: C 290 LYS cc_start: 0.7407 (ttmm) cc_final: 0.7067 (tptt) REVERT: D 169 MET cc_start: 0.0246 (ppp) cc_final: -0.0994 (ppp) REVERT: D 290 LYS cc_start: 0.7410 (ttmm) cc_final: 0.7069 (tptt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1156 time to fit residues: 59.5851 Evaluate side-chains 253 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN C 265 ASN D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145901 restraints weight = 24110.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139624 restraints weight = 65714.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133790 restraints weight = 36510.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133903 restraints weight = 30299.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134355 restraints weight = 16451.107| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 21804 Z= 0.311 Angle : 0.709 8.969 29584 Z= 0.381 Chirality : 0.048 0.167 3404 Planarity : 0.005 0.039 3668 Dihedral : 5.212 28.331 2864 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 1.01 % Allowed : 7.98 % Favored : 91.01 % 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 aren not related in a simple way. whole: -2.39 (0.15), residues: 2616 helix: -0.15 (0.14), residues: 1276 sheet: -3.81 (0.37), residues: 164 loop : -2.95 (0.14), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 336 TYR 0.022 0.002 TYR D 460 PHE 0.017 0.002 PHE C 660 TRP 0.013 0.002 TRP D 388 HIS 0.005 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00771 (21804) covalent geometry : angle 0.70862 (29584) hydrogen bonds : bond 0.06819 ( 920) hydrogen bonds : angle 4.91776 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 0.792 Fit side-chains REVERT: A 169 MET cc_start: -0.0628 (ppp) cc_final: -0.1351 (ppp) REVERT: B 169 MET cc_start: -0.0613 (ppp) cc_final: -0.1335 (ppp) REVERT: C 169 MET cc_start: -0.0625 (ppp) cc_final: -0.1347 (ppp) REVERT: D 169 MET cc_start: -0.0653 (ppp) cc_final: -0.1367 (ppp) REVERT: D 473 GLN cc_start: 0.8198 (tp40) cc_final: 0.7835 (tt0) outliers start: 24 outliers final: 20 residues processed: 285 average time/residue: 0.1066 time to fit residues: 50.5731 Evaluate side-chains 280 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 146 optimal weight: 30.0000 chunk 190 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 151 optimal weight: 0.2980 chunk 170 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.179286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157244 restraints weight = 23477.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151762 restraints weight = 41620.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147089 restraints weight = 45622.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147768 restraints weight = 41321.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146645 restraints weight = 28072.285| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21804 Z= 0.113 Angle : 0.540 7.590 29584 Z= 0.289 Chirality : 0.041 0.165 3404 Planarity : 0.004 0.038 3668 Dihedral : 4.753 30.263 2864 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.20 % Rotamer: Outliers : 1.64 % Allowed : 10.84 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -1.93 (0.16), residues: 2616 helix: 0.39 (0.15), residues: 1284 sheet: -3.73 (0.37), residues: 164 loop : -2.93 (0.14), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.013 0.001 TYR A 288 PHE 0.015 0.001 PHE C 93 TRP 0.012 0.001 TRP D 388 HIS 0.003 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00261 (21804) covalent geometry : angle 0.54047 (29584) hydrogen bonds : bond 0.04257 ( 920) hydrogen bonds : angle 4.32496 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.785 Fit side-chains REVERT: A 169 MET cc_start: -0.0372 (ppp) cc_final: -0.1156 (ppp) REVERT: A 339 ASP cc_start: 0.7489 (t0) cc_final: 0.7260 (t0) REVERT: B 169 MET cc_start: -0.0370 (ppp) cc_final: -0.1151 (ppp) REVERT: B 339 ASP cc_start: 0.7493 (t0) cc_final: 0.7264 (t0) REVERT: C 169 MET cc_start: -0.0368 (ppp) cc_final: -0.1150 (ppp) REVERT: C 339 ASP cc_start: 0.7486 (t0) cc_final: 0.7259 (t0) REVERT: D 169 MET cc_start: -0.0388 (ppp) cc_final: -0.1166 (ppp) REVERT: D 339 ASP cc_start: 0.7486 (t0) cc_final: 0.7258 (t0) REVERT: D 473 GLN cc_start: 0.8170 (tp40) cc_final: 0.7774 (tt0) outliers start: 39 outliers final: 19 residues processed: 304 average time/residue: 0.1185 time to fit residues: 60.4814 Evaluate side-chains 280 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 45 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 14 optimal weight: 30.0000 chunk 251 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 206 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151582 restraints weight = 23447.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151775 restraints weight = 66594.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150634 restraints weight = 31363.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149458 restraints weight = 27131.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150265 restraints weight = 20239.837| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21804 Z= 0.111 Angle : 0.512 7.613 29584 Z= 0.275 Chirality : 0.040 0.139 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.570 29.604 2864 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.80 % Favored : 92.05 % Rotamer: Outliers : 1.72 % Allowed : 12.65 % Favored : 85.63 % 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 aren not related in a simple way. whole: -1.68 (0.16), residues: 2616 helix: 0.67 (0.15), residues: 1284 sheet: -3.67 (0.38), residues: 164 loop : -2.90 (0.14), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 631 TYR 0.008 0.001 TYR C 288 PHE 0.015 0.001 PHE D 93 TRP 0.010 0.001 TRP A 388 HIS 0.003 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00256 (21804) covalent geometry : angle 0.51163 (29584) hydrogen bonds : bond 0.03997 ( 920) hydrogen bonds : angle 4.16370 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.7545 (t0) cc_final: 0.7263 (t0) REVERT: B 339 ASP cc_start: 0.7550 (t0) cc_final: 0.7264 (t0) REVERT: C 339 ASP cc_start: 0.7531 (t0) cc_final: 0.7253 (t0) REVERT: D 339 ASP cc_start: 0.7549 (t0) cc_final: 0.7269 (t0) REVERT: D 473 GLN cc_start: 0.8129 (tp40) cc_final: 0.7770 (tt0) outliers start: 41 outliers final: 30 residues processed: 291 average time/residue: 0.1129 time to fit residues: 55.0325 Evaluate side-chains 283 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 146 optimal weight: 0.0980 chunk 152 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN D 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.179001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.164540 restraints weight = 23449.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160096 restraints weight = 41434.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156409 restraints weight = 40794.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145518 restraints weight = 47151.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142288 restraints weight = 33492.065| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.114 Angle : 0.504 7.267 29584 Z= 0.272 Chirality : 0.041 0.137 3404 Planarity : 0.003 0.039 3668 Dihedral : 4.507 29.075 2864 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.19 % Favored : 92.66 % Rotamer: Outliers : 1.81 % Allowed : 13.32 % Favored : 84.87 % 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 aren not related in a simple way. whole: -1.58 (0.16), residues: 2616 helix: 0.79 (0.15), residues: 1284 sheet: -3.70 (0.37), residues: 164 loop : -2.87 (0.14), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 631 TYR 0.010 0.001 TYR C 288 PHE 0.016 0.001 PHE B 93 TRP 0.009 0.001 TRP D 388 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00270 (21804) covalent geometry : angle 0.50365 (29584) hydrogen bonds : bond 0.03880 ( 920) hydrogen bonds : angle 4.04226 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.613 Fit side-chains REVERT: A 339 ASP cc_start: 0.7543 (t0) cc_final: 0.7275 (t0) REVERT: B 339 ASP cc_start: 0.7528 (t0) cc_final: 0.7260 (t0) REVERT: C 339 ASP cc_start: 0.7549 (t0) cc_final: 0.7287 (t0) REVERT: D 339 ASP cc_start: 0.7562 (t0) cc_final: 0.7302 (t0) REVERT: D 473 GLN cc_start: 0.8113 (tp40) cc_final: 0.7812 (tt0) outliers start: 43 outliers final: 37 residues processed: 286 average time/residue: 0.1107 time to fit residues: 52.7382 Evaluate side-chains 288 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 200 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 214 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166689 restraints weight = 23432.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158370 restraints weight = 43044.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153513 restraints weight = 66401.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152460 restraints weight = 51137.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151073 restraints weight = 34577.793| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21804 Z= 0.119 Angle : 0.504 8.451 29584 Z= 0.271 Chirality : 0.041 0.135 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.461 28.209 2864 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.09 % Rotamer: Outliers : 2.18 % Allowed : 14.24 % Favored : 83.57 % 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 aren not related in a simple way. whole: -1.51 (0.16), residues: 2616 helix: 0.81 (0.15), residues: 1312 sheet: -3.75 (0.37), residues: 164 loop : -2.88 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 643 TYR 0.011 0.001 TYR A 288 PHE 0.014 0.001 PHE C 93 TRP 0.009 0.001 TRP A 388 HIS 0.002 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00284 (21804) covalent geometry : angle 0.50428 (29584) hydrogen bonds : bond 0.03915 ( 920) hydrogen bonds : angle 3.99355 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.796 Fit side-chains REVERT: A 278 ILE cc_start: 0.7918 (pt) cc_final: 0.7661 (pt) REVERT: A 290 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7117 (tptt) REVERT: A 339 ASP cc_start: 0.7600 (t0) cc_final: 0.7279 (t0) REVERT: B 278 ILE cc_start: 0.7913 (pt) cc_final: 0.7653 (pt) REVERT: B 290 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7116 (tptt) REVERT: B 339 ASP cc_start: 0.7601 (t0) cc_final: 0.7281 (t0) REVERT: C 278 ILE cc_start: 0.7919 (pt) cc_final: 0.7670 (pt) REVERT: C 339 ASP cc_start: 0.7594 (t0) cc_final: 0.7287 (t0) REVERT: D 278 ILE cc_start: 0.7910 (pt) cc_final: 0.7650 (pt) REVERT: D 339 ASP cc_start: 0.7604 (t0) cc_final: 0.7292 (t0) REVERT: D 473 GLN cc_start: 0.8122 (tp40) cc_final: 0.7751 (tt0) outliers start: 52 outliers final: 44 residues processed: 294 average time/residue: 0.1069 time to fit residues: 52.5517 Evaluate side-chains 302 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 191 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 210 optimal weight: 0.0470 chunk 237 optimal weight: 0.5980 chunk 151 optimal weight: 0.0370 chunk 223 optimal weight: 5.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.182127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149527 restraints weight = 23963.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150860 restraints weight = 62975.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150983 restraints weight = 28404.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150632 restraints weight = 22140.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153101 restraints weight = 16197.600| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21804 Z= 0.090 Angle : 0.484 7.378 29584 Z= 0.261 Chirality : 0.039 0.135 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.301 28.466 2864 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.72 % Favored : 92.13 % Rotamer: Outliers : 1.43 % Allowed : 15.55 % Favored : 83.03 % 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 aren not related in a simple way. whole: -1.26 (0.16), residues: 2616 helix: 1.07 (0.15), residues: 1304 sheet: -3.76 (0.37), residues: 164 loop : -2.76 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 333 TYR 0.016 0.001 TYR A 288 PHE 0.017 0.001 PHE B 93 TRP 0.010 0.001 TRP D 388 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00200 (21804) covalent geometry : angle 0.48410 (29584) hydrogen bonds : bond 0.03159 ( 920) hydrogen bonds : angle 3.81198 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.808 Fit side-chains REVERT: A 278 ILE cc_start: 0.7710 (pt) cc_final: 0.7444 (pt) REVERT: A 290 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7034 (tptt) REVERT: A 339 ASP cc_start: 0.7520 (t0) cc_final: 0.7227 (t0) REVERT: B 278 ILE cc_start: 0.7711 (pt) cc_final: 0.7442 (pt) REVERT: B 290 LYS cc_start: 0.7676 (ttmm) cc_final: 0.7027 (tptt) REVERT: B 339 ASP cc_start: 0.7526 (t0) cc_final: 0.7232 (t0) REVERT: C 278 ILE cc_start: 0.7709 (pt) cc_final: 0.7465 (pt) REVERT: C 290 LYS cc_start: 0.7625 (ttmm) cc_final: 0.6984 (tptt) REVERT: C 339 ASP cc_start: 0.7519 (t0) cc_final: 0.7227 (t0) REVERT: D 278 ILE cc_start: 0.7700 (pt) cc_final: 0.7453 (pt) REVERT: D 290 LYS cc_start: 0.7630 (ttmm) cc_final: 0.6992 (tptt) REVERT: D 339 ASP cc_start: 0.7503 (t0) cc_final: 0.7211 (t0) REVERT: D 473 GLN cc_start: 0.8066 (tp40) cc_final: 0.7698 (tt0) outliers start: 34 outliers final: 25 residues processed: 279 average time/residue: 0.1214 time to fit residues: 56.2411 Evaluate side-chains 269 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 255 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.180107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146892 restraints weight = 23858.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147973 restraints weight = 65225.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148200 restraints weight = 31187.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147991 restraints weight = 22134.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150467 restraints weight = 16218.711| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21804 Z= 0.132 Angle : 0.514 7.909 29584 Z= 0.278 Chirality : 0.041 0.207 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.415 27.845 2864 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 1.72 % Allowed : 14.66 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.16), residues: 2616 helix: 0.92 (0.15), residues: 1316 sheet: -3.73 (0.37), residues: 164 loop : -2.77 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 643 TYR 0.020 0.001 TYR B 288 PHE 0.014 0.001 PHE C 93 TRP 0.007 0.001 TRP C 388 HIS 0.004 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00320 (21804) covalent geometry : angle 0.51364 (29584) hydrogen bonds : bond 0.03964 ( 920) hydrogen bonds : angle 3.90897 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.751 Fit side-chains REVERT: A 278 ILE cc_start: 0.7836 (pt) cc_final: 0.7580 (pt) REVERT: A 339 ASP cc_start: 0.7553 (t0) cc_final: 0.7221 (t0) REVERT: B 278 ILE cc_start: 0.7835 (pt) cc_final: 0.7574 (pt) REVERT: B 339 ASP cc_start: 0.7542 (t0) cc_final: 0.7212 (t0) REVERT: C 278 ILE cc_start: 0.7859 (pt) cc_final: 0.7605 (pt) REVERT: C 290 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7038 (tptt) REVERT: C 339 ASP cc_start: 0.7532 (t0) cc_final: 0.7208 (t0) REVERT: D 278 ILE cc_start: 0.7842 (pt) cc_final: 0.7592 (pt) REVERT: D 290 LYS cc_start: 0.7676 (ttmm) cc_final: 0.7045 (tptt) REVERT: D 339 ASP cc_start: 0.7545 (t0) cc_final: 0.7216 (t0) REVERT: D 473 GLN cc_start: 0.8090 (tp40) cc_final: 0.7796 (tt0) outliers start: 41 outliers final: 31 residues processed: 268 average time/residue: 0.1203 time to fit residues: 53.3852 Evaluate side-chains 276 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 139 optimal weight: 0.0060 chunk 129 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154969 restraints weight = 23939.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141461 restraints weight = 44913.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136055 restraints weight = 58463.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137582 restraints weight = 43861.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138115 restraints weight = 23213.026| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21804 Z= 0.155 Angle : 0.541 7.274 29584 Z= 0.292 Chirality : 0.042 0.183 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.590 28.189 2864 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 1.76 % Allowed : 15.55 % Favored : 82.69 % 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 aren not related in a simple way. whole: -1.46 (0.16), residues: 2616 helix: 0.80 (0.15), residues: 1312 sheet: -3.74 (0.36), residues: 164 loop : -2.77 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 336 TYR 0.013 0.001 TYR C 288 PHE 0.015 0.001 PHE B 93 TRP 0.007 0.001 TRP D 219 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00379 (21804) covalent geometry : angle 0.54091 (29584) hydrogen bonds : bond 0.04398 ( 920) hydrogen bonds : angle 4.01583 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.678 Fit side-chains REVERT: A 339 ASP cc_start: 0.7661 (t0) cc_final: 0.7375 (t0) REVERT: B 339 ASP cc_start: 0.7652 (t0) cc_final: 0.7363 (t0) REVERT: C 290 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7004 (tptt) REVERT: C 339 ASP cc_start: 0.7634 (t0) cc_final: 0.7343 (t0) REVERT: D 290 LYS cc_start: 0.7813 (ttmm) cc_final: 0.6992 (tptt) REVERT: D 339 ASP cc_start: 0.7669 (t0) cc_final: 0.7377 (t0) REVERT: D 473 GLN cc_start: 0.8096 (tp40) cc_final: 0.7759 (tt0) outliers start: 42 outliers final: 34 residues processed: 279 average time/residue: 0.1105 time to fit residues: 50.8702 Evaluate side-chains 276 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 88 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 261 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 183 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS B 579 HIS D 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.181680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.168355 restraints weight = 23656.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156621 restraints weight = 43071.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151061 restraints weight = 65700.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150257 restraints weight = 48178.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.149170 restraints weight = 35159.163| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21804 Z= 0.094 Angle : 0.491 7.515 29584 Z= 0.265 Chirality : 0.040 0.149 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.406 28.717 2864 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.39 % Rotamer: Outliers : 1.09 % Allowed : 16.43 % Favored : 82.48 % 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 aren not related in a simple way. whole: -1.23 (0.16), residues: 2616 helix: 1.04 (0.15), residues: 1308 sheet: -3.78 (0.36), residues: 164 loop : -2.69 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 333 TYR 0.021 0.001 TYR C 288 PHE 0.017 0.001 PHE C 93 TRP 0.011 0.001 TRP C 388 HIS 0.004 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00214 (21804) covalent geometry : angle 0.49065 (29584) hydrogen bonds : bond 0.03359 ( 920) hydrogen bonds : angle 3.78912 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.703 Fit side-chains REVERT: A 278 ILE cc_start: 0.7798 (pt) cc_final: 0.7518 (pt) REVERT: A 339 ASP cc_start: 0.7562 (t0) cc_final: 0.7275 (t0) REVERT: A 386 ASP cc_start: 0.8098 (p0) cc_final: 0.7771 (p0) REVERT: B 278 ILE cc_start: 0.7791 (pt) cc_final: 0.7509 (pt) REVERT: B 339 ASP cc_start: 0.7547 (t0) cc_final: 0.7255 (t0) REVERT: B 386 ASP cc_start: 0.8097 (p0) cc_final: 0.7766 (p0) REVERT: C 278 ILE cc_start: 0.7846 (pt) cc_final: 0.7532 (pt) REVERT: C 339 ASP cc_start: 0.7536 (t0) cc_final: 0.7252 (t0) REVERT: C 386 ASP cc_start: 0.8099 (p0) cc_final: 0.7769 (p0) REVERT: D 278 ILE cc_start: 0.7799 (pt) cc_final: 0.7485 (pt) REVERT: D 339 ASP cc_start: 0.7551 (t0) cc_final: 0.7274 (t0) REVERT: D 386 ASP cc_start: 0.8093 (p0) cc_final: 0.7767 (p0) REVERT: D 473 GLN cc_start: 0.8020 (tp40) cc_final: 0.7712 (tt0) outliers start: 26 outliers final: 22 residues processed: 278 average time/residue: 0.1095 time to fit residues: 50.4346 Evaluate side-chains 261 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 206 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.0370 chunk 164 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.182323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.155173 restraints weight = 23263.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154177 restraints weight = 62895.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150792 restraints weight = 28588.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149907 restraints weight = 28920.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150982 restraints weight = 16748.689| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21804 Z= 0.117 Angle : 0.522 9.825 29584 Z= 0.277 Chirality : 0.041 0.186 3404 Planarity : 0.004 0.058 3668 Dihedral : 4.437 28.179 2864 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 1.13 % Allowed : 16.97 % Favored : 81.89 % 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 aren not related in a simple way. whole: -1.26 (0.16), residues: 2616 helix: 0.99 (0.15), residues: 1316 sheet: -3.78 (0.36), residues: 164 loop : -2.70 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 401 TYR 0.008 0.001 TYR D 424 PHE 0.017 0.001 PHE B 93 TRP 0.008 0.001 TRP D 388 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00277 (21804) covalent geometry : angle 0.52198 (29584) hydrogen bonds : bond 0.03703 ( 920) hydrogen bonds : angle 3.83254 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.07 seconds wall clock time: 48 minutes 21.65 seconds (2901.65 seconds total)