Starting phenix.real_space_refine on Wed Jun 18 12:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yif_33857/06_2025/7yif_33857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yif_33857/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yif_33857/06_2025/7yif_33857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yif_33857/06_2025/7yif_33857.map" model { file = "/net/cci-nas-00/data/ceres_data/7yif_33857/06_2025/7yif_33857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yif_33857/06_2025/7yif_33857.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.25, per 1000 atoms: 0.62 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: 4.49 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.55 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: 7.85 Time building geometry restraints manager: 5.48 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.690 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 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: 0.030 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (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 TRP 0.013 0.001 TRP D 217 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.001 PHE D 226 TYR 0.011 0.001 TYR A 460 ARG 0.009 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.18382 ( 920) hydrogen bonds : angle 5.89250 ( 2640) covalent geometry : bond 0.00220 (21804) covalent geometry : angle 0.57616 (29584) *********************** 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 : 2.458 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: 0.2766 time to fit residues: 142.8176 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 : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.180886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150744 restraints weight = 23945.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150096 restraints weight = 64117.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146054 restraints weight = 28370.913| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1037 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= 0.135 Angle : 0.550 8.269 29584 Z= 0.295 Chirality : 0.041 0.138 3404 Planarity : 0.004 0.038 3668 Dihedral : 4.600 30.151 2864 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 1.13 % Allowed : 5.92 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2616 helix: 0.39 (0.15), residues: 1284 sheet: -3.71 (0.38), residues: 164 loop : -2.76 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 217 HIS 0.004 0.001 HIS C 176 PHE 0.016 0.002 PHE C 93 TYR 0.011 0.001 TYR C 460 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 920) hydrogen bonds : angle 4.41654 ( 2640) covalent geometry : bond 0.00314 (21804) covalent geometry : angle 0.55042 (29584) *********************** 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 303 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 2.336 Fit side-chains REVERT: A 169 MET cc_start: -0.0493 (ppp) cc_final: -0.1256 (ppp) REVERT: B 169 MET cc_start: -0.0489 (ppp) cc_final: -0.1247 (ppp) REVERT: C 169 MET cc_start: -0.0443 (ppp) cc_final: -0.1199 (ppp) REVERT: D 169 MET cc_start: -0.0521 (ppp) cc_final: -0.1275 (ppp) REVERT: D 473 GLN cc_start: 0.8209 (tp40) cc_final: 0.7852 (tt0) outliers start: 27 outliers final: 20 residues processed: 288 average time/residue: 0.2776 time to fit residues: 132.3025 Evaluate side-chains 273 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 167 optimal weight: 5.9990 chunk 23 optimal weight: 0.0270 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.183150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.161264 restraints weight = 23363.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.155046 restraints weight = 44099.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151433 restraints weight = 42288.551| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1417 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= 0.100 Angle : 0.498 6.976 29584 Z= 0.269 Chirality : 0.040 0.136 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.466 30.688 2864 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.20 % Rotamer: Outliers : 0.84 % Allowed : 10.13 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2616 helix: 0.65 (0.15), residues: 1288 sheet: -3.71 (0.37), residues: 164 loop : -2.76 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.003 0.001 HIS A 176 PHE 0.016 0.001 PHE D 93 TYR 0.012 0.001 TYR A 288 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 920) hydrogen bonds : angle 4.13029 ( 2640) covalent geometry : bond 0.00223 (21804) covalent geometry : angle 0.49817 (29584) *********************** 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 292 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 2.552 Fit side-chains REVERT: A 169 MET cc_start: -0.0229 (ppp) cc_final: -0.1019 (ppp) REVERT: B 169 MET cc_start: -0.0227 (ppp) cc_final: -0.1018 (ppp) REVERT: C 169 MET cc_start: -0.0245 (ppp) cc_final: -0.1036 (ppp) REVERT: D 169 MET cc_start: -0.0247 (ppp) cc_final: -0.1034 (ppp) REVERT: D 473 GLN cc_start: 0.8138 (tp40) cc_final: 0.7767 (tt0) outliers start: 20 outliers final: 8 residues processed: 276 average time/residue: 0.2995 time to fit residues: 137.9935 Evaluate side-chains 265 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 207 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 198 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3993 r_free = 0.3993 target = 0.182492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.153772 restraints weight = 23555.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154200 restraints weight = 67657.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.154579 restraints weight = 32980.259| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1618 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= 0.121 Angle : 0.520 7.885 29584 Z= 0.275 Chirality : 0.040 0.134 3404 Planarity : 0.003 0.038 3668 Dihedral : 4.427 29.024 2864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.09 % Rotamer: Outliers : 1.72 % Allowed : 11.72 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2616 helix: 0.72 (0.15), residues: 1288 sheet: -3.59 (0.38), residues: 164 loop : -2.74 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 388 HIS 0.003 0.001 HIS B 176 PHE 0.015 0.001 PHE C 93 TYR 0.009 0.001 TYR B 460 ARG 0.002 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 920) hydrogen bonds : angle 4.05949 ( 2640) covalent geometry : bond 0.00287 (21804) covalent geometry : angle 0.51985 (29584) *********************** 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 299 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 2.329 Fit side-chains REVERT: A 169 MET cc_start: -0.0408 (ppp) cc_final: -0.1149 (ppp) REVERT: A 265 ASN cc_start: 0.7924 (t0) cc_final: 0.7500 (m-40) REVERT: A 286 MET cc_start: 0.6678 (tpp) cc_final: 0.6406 (tpp) REVERT: A 339 ASP cc_start: 0.7509 (t0) cc_final: 0.7189 (t0) REVERT: B 169 MET cc_start: -0.0408 (ppp) cc_final: -0.1149 (ppp) REVERT: B 265 ASN cc_start: 0.7913 (t0) cc_final: 0.7497 (m-40) REVERT: B 286 MET cc_start: 0.6671 (tpp) cc_final: 0.6401 (tpp) REVERT: B 339 ASP cc_start: 0.7521 (t0) cc_final: 0.7199 (t0) REVERT: C 169 MET cc_start: -0.0417 (ppp) cc_final: -0.1152 (ppp) REVERT: C 339 ASP cc_start: 0.7486 (t0) cc_final: 0.7162 (t0) REVERT: D 169 MET cc_start: -0.0420 (ppp) cc_final: -0.1162 (ppp) REVERT: D 265 ASN cc_start: 0.7913 (t0) cc_final: 0.7486 (m-40) REVERT: D 286 MET cc_start: 0.6690 (tpp) cc_final: 0.6416 (tpp) REVERT: D 339 ASP cc_start: 0.7520 (t0) cc_final: 0.7201 (t0) REVERT: D 473 GLN cc_start: 0.8171 (tp40) cc_final: 0.7832 (tt0) outliers start: 41 outliers final: 20 residues processed: 277 average time/residue: 0.2793 time to fit residues: 130.2454 Evaluate side-chains 271 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 268 THR 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 263 VAL Chi-restraints excluded: chain B residue 268 THR 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 207 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 51 optimal weight: 0.0470 chunk 144 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 133 optimal weight: 0.0040 chunk 212 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3997 r_free = 0.3997 target = 0.184095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.158731 restraints weight = 23848.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.151713 restraints weight = 58984.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.144697 restraints weight = 36285.075| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21804 Z= 0.100 Angle : 0.492 7.024 29584 Z= 0.262 Chirality : 0.040 0.152 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.361 29.334 2864 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.03 % Favored : 92.81 % Rotamer: Outliers : 1.39 % Allowed : 13.40 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2616 helix: 0.90 (0.15), residues: 1292 sheet: -3.60 (0.37), residues: 164 loop : -2.66 (0.14), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 388 HIS 0.003 0.001 HIS B 176 PHE 0.017 0.001 PHE D 93 TYR 0.007 0.001 TYR A 341 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 920) hydrogen bonds : angle 3.90315 ( 2640) covalent geometry : bond 0.00232 (21804) covalent geometry : angle 0.49237 (29584) *********************** 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 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 2.469 Fit side-chains REVERT: A 286 MET cc_start: 0.6755 (tpp) cc_final: 0.6450 (tpp) REVERT: A 339 ASP cc_start: 0.7683 (t0) cc_final: 0.7375 (t0) REVERT: B 286 MET cc_start: 0.6754 (tpp) cc_final: 0.6449 (tpp) REVERT: B 339 ASP cc_start: 0.7696 (t0) cc_final: 0.7395 (t0) REVERT: C 286 MET cc_start: 0.6798 (tpp) cc_final: 0.6461 (tpp) REVERT: C 339 ASP cc_start: 0.7661 (t0) cc_final: 0.7358 (t0) REVERT: D 286 MET cc_start: 0.6762 (tpp) cc_final: 0.6452 (tpp) REVERT: D 339 ASP cc_start: 0.7684 (t0) cc_final: 0.7381 (t0) REVERT: D 473 GLN cc_start: 0.8100 (tp40) cc_final: 0.7649 (tt0) outliers start: 33 outliers final: 25 residues processed: 283 average time/residue: 0.2665 time to fit residues: 126.3052 Evaluate side-chains 272 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 472 GLN Chi-restraints excluded: chain A residue 484 MET 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 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE 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 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 484 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 30.0000 chunk 67 optimal weight: 0.0970 chunk 144 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3982 r_free = 0.3982 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.168083 restraints weight = 23288.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157658 restraints weight = 38385.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153446 restraints weight = 64729.289| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1882 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= 0.124 Angle : 0.511 8.479 29584 Z= 0.273 Chirality : 0.041 0.148 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.386 28.423 2864 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 1.60 % Allowed : 13.45 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2616 helix: 0.86 (0.15), residues: 1320 sheet: -3.63 (0.37), residues: 164 loop : -2.71 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 388 HIS 0.002 0.001 HIS C 176 PHE 0.015 0.001 PHE C 93 TYR 0.016 0.001 TYR B 288 ARG 0.001 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 920) hydrogen bonds : angle 3.91361 ( 2640) covalent geometry : bond 0.00299 (21804) covalent geometry : angle 0.51128 (29584) *********************** 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 291 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 2.190 Fit side-chains REVERT: A 339 ASP cc_start: 0.7520 (t0) cc_final: 0.7214 (t0) REVERT: B 339 ASP cc_start: 0.7526 (t0) cc_final: 0.7223 (t0) REVERT: C 339 ASP cc_start: 0.7474 (t0) cc_final: 0.7168 (t0) REVERT: D 339 ASP cc_start: 0.7535 (t0) cc_final: 0.7233 (t0) REVERT: D 473 GLN cc_start: 0.8073 (tp40) cc_final: 0.7726 (tt0) outliers start: 38 outliers final: 26 residues processed: 273 average time/residue: 0.2670 time to fit residues: 121.4941 Evaluate side-chains 265 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 472 GLN Chi-restraints excluded: chain A residue 484 MET 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 484 MET 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 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 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3993 r_free = 0.3993 target = 0.182197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153079 restraints weight = 23246.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153654 restraints weight = 67183.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153698 restraints weight = 31523.481| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1971 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= 0.118 Angle : 0.512 7.760 29584 Z= 0.276 Chirality : 0.040 0.161 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.416 28.417 2864 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.42 % Favored : 92.43 % Rotamer: Outliers : 1.85 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2616 helix: 0.95 (0.15), residues: 1316 sheet: -3.72 (0.36), residues: 164 loop : -2.74 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 388 HIS 0.004 0.001 HIS B 176 PHE 0.016 0.001 PHE C 93 TYR 0.012 0.001 TYR B 288 ARG 0.001 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 920) hydrogen bonds : angle 3.85972 ( 2640) covalent geometry : bond 0.00282 (21804) covalent geometry : angle 0.51249 (29584) *********************** 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 283 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 2.487 Fit side-chains REVERT: A 169 MET cc_start: -0.0277 (ppp) cc_final: -0.0707 (ptp) REVERT: A 339 ASP cc_start: 0.7488 (t0) cc_final: 0.7178 (t0) REVERT: B 169 MET cc_start: -0.0267 (ppp) cc_final: -0.0692 (ptp) REVERT: B 339 ASP cc_start: 0.7497 (t0) cc_final: 0.7181 (t0) REVERT: C 169 MET cc_start: -0.0292 (ppp) cc_final: -0.0718 (ptp) REVERT: C 278 ILE cc_start: 0.7896 (pt) cc_final: 0.7657 (pt) REVERT: C 339 ASP cc_start: 0.7503 (t0) cc_final: 0.7182 (t0) REVERT: D 169 MET cc_start: -0.0286 (ppp) cc_final: -0.0710 (ptp) REVERT: D 339 ASP cc_start: 0.7509 (t0) cc_final: 0.7193 (t0) REVERT: D 473 GLN cc_start: 0.8087 (tp40) cc_final: 0.7806 (tt0) outliers start: 44 outliers final: 33 residues processed: 266 average time/residue: 0.3668 time to fit residues: 166.2176 Evaluate side-chains 264 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 207 ILE 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 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 207 ILE 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 484 MET Chi-restraints excluded: chain C residue 65 CYS 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 277 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 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 484 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 160 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 173 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3977 r_free = 0.3977 target = 0.180260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146688 restraints weight = 23882.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147527 restraints weight = 65545.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146983 restraints weight = 30816.382| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2019 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= 0.120 Angle : 0.510 7.792 29584 Z= 0.274 Chirality : 0.040 0.139 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.396 28.164 2864 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 1.43 % Allowed : 15.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2616 helix: 0.96 (0.15), residues: 1316 sheet: -3.73 (0.36), residues: 164 loop : -2.74 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 388 HIS 0.004 0.001 HIS A 176 PHE 0.016 0.001 PHE C 93 TYR 0.017 0.001 TYR B 288 ARG 0.001 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 920) hydrogen bonds : angle 3.84836 ( 2640) covalent geometry : bond 0.00285 (21804) covalent geometry : angle 0.50989 (29584) *********************** 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 263 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 5.403 Fit side-chains REVERT: A 169 MET cc_start: -0.0465 (ppp) cc_final: -0.0862 (ptp) REVERT: A 278 ILE cc_start: 0.7899 (pt) cc_final: 0.7659 (pt) REVERT: A 339 ASP cc_start: 0.7621 (t0) cc_final: 0.7297 (t0) REVERT: B 169 MET cc_start: -0.0456 (ppp) cc_final: -0.0859 (ptp) REVERT: B 339 ASP cc_start: 0.7622 (t0) cc_final: 0.7302 (t0) REVERT: C 169 MET cc_start: -0.0467 (ppp) cc_final: -0.0864 (ptp) REVERT: C 278 ILE cc_start: 0.7872 (pt) cc_final: 0.7621 (pt) REVERT: C 339 ASP cc_start: 0.7602 (t0) cc_final: 0.7284 (t0) REVERT: D 169 MET cc_start: -0.0465 (ppp) cc_final: -0.0861 (ptp) REVERT: D 278 ILE cc_start: 0.7894 (pt) cc_final: 0.7654 (pt) REVERT: D 339 ASP cc_start: 0.7624 (t0) cc_final: 0.7300 (t0) REVERT: D 473 GLN cc_start: 0.8114 (tp40) cc_final: 0.7802 (tt0) outliers start: 34 outliers final: 30 residues processed: 253 average time/residue: 0.3326 time to fit residues: 140.8108 Evaluate side-chains 254 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 207 ILE 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 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 207 ILE 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 484 MET Chi-restraints excluded: chain C residue 65 CYS 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 277 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 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 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE 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 71 optimal weight: 0.3980 chunk 154 optimal weight: 0.7980 chunk 199 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 263 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4033 r_free = 0.4033 target = 0.185950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173217 restraints weight = 23721.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160720 restraints weight = 41631.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153831 restraints weight = 73654.404| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21804 Z= 0.102 Angle : 0.493 7.572 29584 Z= 0.265 Chirality : 0.040 0.167 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.329 28.468 2864 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.42 % Favored : 92.43 % Rotamer: Outliers : 1.13 % Allowed : 15.55 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2616 helix: 1.05 (0.15), residues: 1316 sheet: -3.73 (0.36), residues: 164 loop : -2.70 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.004 0.001 HIS B 176 PHE 0.017 0.001 PHE B 93 TYR 0.015 0.001 TYR D 288 ARG 0.001 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 920) hydrogen bonds : angle 3.74708 ( 2640) covalent geometry : bond 0.00236 (21804) covalent geometry : angle 0.49338 (29584) *********************** 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 263 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 2.399 Fit side-chains REVERT: A 169 MET cc_start: -0.0473 (ppp) cc_final: -0.0865 (ptp) REVERT: A 278 ILE cc_start: 0.7886 (pt) cc_final: 0.7638 (pt) REVERT: A 339 ASP cc_start: 0.7635 (t0) cc_final: 0.7342 (t0) REVERT: B 169 MET cc_start: -0.0460 (ppp) cc_final: -0.0850 (ptp) REVERT: B 339 ASP cc_start: 0.7625 (t0) cc_final: 0.7326 (t0) REVERT: C 169 MET cc_start: -0.0472 (ppp) cc_final: -0.0862 (ptp) REVERT: C 278 ILE cc_start: 0.7841 (pt) cc_final: 0.7624 (pt) REVERT: C 290 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7128 (tptt) REVERT: C 339 ASP cc_start: 0.7562 (t0) cc_final: 0.7273 (t0) REVERT: D 169 MET cc_start: -0.0470 (ppp) cc_final: -0.0859 (ptp) REVERT: D 278 ILE cc_start: 0.7885 (pt) cc_final: 0.7641 (pt) REVERT: D 339 ASP cc_start: 0.7651 (t0) cc_final: 0.7364 (t0) REVERT: D 473 GLN cc_start: 0.8214 (tp40) cc_final: 0.7753 (tt0) outliers start: 27 outliers final: 26 residues processed: 253 average time/residue: 0.2783 time to fit residues: 116.8731 Evaluate side-chains 253 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 207 ILE 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 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 207 ILE 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 484 MET Chi-restraints excluded: chain C residue 65 CYS 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 277 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 D residue 65 CYS Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 257 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 182 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3981 r_free = 0.3981 target = 0.180857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156880 restraints weight = 23871.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149592 restraints weight = 45453.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144234 restraints weight = 47235.221| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21804 Z= 0.095 Angle : 0.495 9.978 29584 Z= 0.263 Chirality : 0.040 0.140 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.261 27.685 2864 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 1.09 % Allowed : 15.42 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.16), residues: 2616 helix: 1.12 (0.15), residues: 1316 sheet: -3.72 (0.36), residues: 164 loop : -2.67 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.004 0.001 HIS B 176 PHE 0.017 0.001 PHE A 93 TYR 0.007 0.001 TYR B 288 ARG 0.001 0.000 ARG A 55 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 920) hydrogen bonds : angle 3.69856 ( 2640) covalent geometry : bond 0.00216 (21804) covalent geometry : angle 0.49453 (29584) ********************** 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 255 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 2.417 Fit side-chains REVERT: A 169 MET cc_start: -0.0354 (ppp) cc_final: -0.0721 (ptp) REVERT: A 278 ILE cc_start: 0.7879 (pt) cc_final: 0.7617 (pt) REVERT: A 339 ASP cc_start: 0.7633 (t0) cc_final: 0.7327 (t0) REVERT: B 169 MET cc_start: -0.0347 (ppp) cc_final: -0.0712 (ptp) REVERT: B 339 ASP cc_start: 0.7637 (t0) cc_final: 0.7332 (t0) REVERT: C 169 MET cc_start: -0.0372 (ppp) cc_final: -0.0740 (ptp) REVERT: C 278 ILE cc_start: 0.7805 (pt) cc_final: 0.7594 (pt) REVERT: C 290 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7093 (tptt) REVERT: C 339 ASP cc_start: 0.7600 (t0) cc_final: 0.7294 (t0) REVERT: D 169 MET cc_start: -0.0367 (ppp) cc_final: -0.0732 (ptp) REVERT: D 278 ILE cc_start: 0.7871 (pt) cc_final: 0.7612 (pt) REVERT: D 339 ASP cc_start: 0.7641 (t0) cc_final: 0.7331 (t0) REVERT: D 473 GLN cc_start: 0.8062 (tp40) cc_final: 0.7777 (tt0) outliers start: 26 outliers final: 24 residues processed: 245 average time/residue: 0.2759 time to fit residues: 112.2964 Evaluate side-chains 247 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 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 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 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE 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 484 MET Chi-restraints excluded: chain D residue 65 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 80 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4011 r_free = 0.4011 target = 0.184274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171858 restraints weight = 23303.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160244 restraints weight = 43087.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154952 restraints weight = 73416.692| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2147 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= 0.107 Angle : 0.505 9.780 29584 Z= 0.268 Chirality : 0.040 0.185 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.283 27.542 2864 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 1.01 % Allowed : 15.71 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2616 helix: 1.13 (0.15), residues: 1316 sheet: -3.73 (0.36), residues: 164 loop : -2.63 (0.15), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.004 0.001 HIS A 176 PHE 0.017 0.001 PHE C 93 TYR 0.007 0.001 TYR D 653 ARG 0.001 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 920) hydrogen bonds : angle 3.71063 ( 2640) covalent geometry : bond 0.00251 (21804) covalent geometry : angle 0.50505 (29584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6319.90 seconds wall clock time: 112 minutes 46.40 seconds (6766.40 seconds total)