Starting phenix.real_space_refine on Mon Apr 6 04:36:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2k_23131/04_2026/7l2k_23131.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10494 2.51 5 N 2588 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3998 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.43, per 1000 atoms: 0.21 Number of scatterers: 15998 At special positions: 0 Unit cell: (127.65, 127.65, 111.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2816 8.00 N 2588 7.00 C 10494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 647.7 milliseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 4 sheets defined 68.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.738A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.616A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.919A pdb=" N VAL A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.767A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.848A pdb=" N SER A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.005A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.797A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.537A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 498 removed outlier: 3.600A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 532 removed outlier: 4.262A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.708A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.666A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 599 removed outlier: 4.919A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.941A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.512A pdb=" N ASN A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.662A pdb=" N SER A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.003A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.881A pdb=" N THR C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.647A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.780A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.138A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.534A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.650A pdb=" N TYR C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.592A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.563A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 599 removed outlier: 3.947A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 643 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 3.759A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 216 through 221 removed outlier: 3.662A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.654A pdb=" N THR D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 268 removed outlier: 3.990A pdb=" N LEU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.505A pdb=" N ALA D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.811A pdb=" N SER D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.968A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.740A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 498 removed outlier: 3.623A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.617A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.697A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 599 removed outlier: 4.874A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.942A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 691 through 712 removed outlier: 3.533A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.740A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.759A pdb=" N THR B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.896A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.504A pdb=" N ALA B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.880A pdb=" N SER B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.032A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.787A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 498 removed outlier: 3.610A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.749A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.660A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 599 removed outlier: 4.972A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.960A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 6.053A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.728A pdb=" N SER A 379 " --> pdb=" O TRP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.369A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.516A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 4.086A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4854 1.34 - 1.46: 3547 1.46 - 1.58: 7797 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 16362 Sorted by residual: bond pdb=" C ASN B 652 " pdb=" N TYR B 653 " ideal model delta sigma weight residual 1.332 1.221 0.111 1.40e-02 5.10e+03 6.28e+01 bond pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 1.332 1.258 0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" CA TYR C 555 " pdb=" C TYR C 555 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" C THR C 650 " pdb=" N GLU C 651 " ideal model delta sigma weight residual 1.332 1.368 -0.035 1.29e-02 6.01e+03 7.41e+00 bond pdb=" C ASN D 652 " pdb=" N TYR D 653 " ideal model delta sigma weight residual 1.332 1.295 0.037 1.40e-02 5.10e+03 6.99e+00 ... (remaining 16357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 20858 1.58 - 3.17: 1097 3.17 - 4.75: 160 4.75 - 6.34: 34 6.34 - 7.92: 4 Bond angle restraints: 22153 Sorted by residual: angle pdb=" CA ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 116.43 108.51 7.92 1.37e+00 5.33e-01 3.34e+01 angle pdb=" O ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 122.96 129.66 -6.70 1.26e+00 6.30e-01 2.83e+01 angle pdb=" C THR B 650 " pdb=" N GLU B 651 " pdb=" CA GLU B 651 " ideal model delta sigma weight residual 122.60 116.94 5.66 1.56e+00 4.11e-01 1.32e+01 angle pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C ASN D 652 " pdb=" N TYR D 653 " pdb=" CA TYR D 653 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 ... (remaining 22148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 8899 15.71 - 31.41: 657 31.41 - 47.12: 89 47.12 - 62.83: 24 62.83 - 78.54: 10 Dihedral angle restraints: 9679 sinusoidal: 3839 harmonic: 5840 Sorted by residual: dihedral pdb=" CA PRO A 732 " pdb=" C PRO A 732 " pdb=" N ASP A 733 " pdb=" CA ASP A 733 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 711 " pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR D 389 " pdb=" C THR D 389 " pdb=" N CYS D 390 " pdb=" CA CYS D 390 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1487 0.035 - 0.069: 773 0.069 - 0.104: 224 0.104 - 0.138: 54 0.138 - 0.173: 9 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CG LEU C 637 " pdb=" CB LEU C 637 " pdb=" CD1 LEU C 637 " pdb=" CD2 LEU C 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE B 689 " pdb=" CA ILE B 689 " pdb=" CG1 ILE B 689 " pdb=" CG2 ILE B 689 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CG LEU A 637 " pdb=" CB LEU A 637 " pdb=" CD1 LEU A 637 " pdb=" CD2 LEU A 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2544 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 650 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR C 650 " 0.068 2.00e-02 2.50e+03 pdb=" O THR C 650 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU C 651 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 650 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 650 " -0.064 2.00e-02 2.50e+03 pdb=" O THR B 650 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 651 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 548 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C GLY C 548 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY C 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP C 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 114 2.59 - 3.16: 14465 3.16 - 3.74: 24044 3.74 - 4.32: 32807 4.32 - 4.90: 54071 Nonbonded interactions: 125501 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" O ASP A 733 " model vdw 2.007 3.040 nonbonded pdb=" OG1 THR C 731 " pdb=" O ASP C 733 " model vdw 2.026 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" O ASP D 733 " model vdw 2.029 3.040 nonbonded pdb=" OE1 GLU C 651 " pdb=" NZ LYS C 656 " model vdw 2.073 3.120 nonbonded pdb=" O ILE D 672 " pdb=" ND2 ASN D 676 " model vdw 2.108 3.120 ... (remaining 125496 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 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'B' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'C' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.008 0.111 16362 Z= 0.379 Angle : 0.819 7.921 22153 Z= 0.466 Chirality : 0.044 0.173 2547 Planarity : 0.005 0.040 2724 Dihedral : 11.267 78.535 5911 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.56 % Favored : 93.24 % Rotamer: Outliers : 0.46 % Allowed : 2.45 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1952 helix: 1.07 (0.14), residues: 1196 sheet: 0.16 (0.76), residues: 36 loop : -1.97 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 557 TYR 0.031 0.003 TYR C 565 PHE 0.023 0.003 PHE D 649 TRP 0.013 0.002 TRP A 426 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00786 (16362) covalent geometry : angle 0.81886 (22153) hydrogen bonds : bond 0.13511 ( 926) hydrogen bonds : angle 5.55355 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 772 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7947 (mmm) cc_final: 0.7438 (mmm) REVERT: A 381 LEU cc_start: 0.7967 (mt) cc_final: 0.7594 (mm) REVERT: A 428 ARG cc_start: 0.7477 (mtp180) cc_final: 0.7275 (ptm160) REVERT: A 435 TYR cc_start: 0.8938 (m-10) cc_final: 0.8595 (m-80) REVERT: A 441 TYR cc_start: 0.9334 (t80) cc_final: 0.9126 (t80) REVERT: A 465 LEU cc_start: 0.8514 (mt) cc_final: 0.8151 (pt) REVERT: A 472 TYR cc_start: 0.8043 (m-80) cc_final: 0.7643 (m-80) REVERT: A 504 LYS cc_start: 0.8573 (mttt) cc_final: 0.8330 (ttmt) REVERT: A 515 LEU cc_start: 0.9431 (mt) cc_final: 0.9212 (mt) REVERT: A 517 PHE cc_start: 0.8850 (t80) cc_final: 0.8477 (t80) REVERT: A 536 GLU cc_start: 0.9009 (mp0) cc_final: 0.8596 (mp0) REVERT: A 557 ARG cc_start: 0.8844 (ptp-170) cc_final: 0.8513 (ptp-170) REVERT: A 572 MET cc_start: 0.7601 (tpp) cc_final: 0.7355 (tpp) REVERT: A 631 TYR cc_start: 0.7518 (t80) cc_final: 0.7262 (t80) REVERT: A 634 CYS cc_start: 0.8600 (m) cc_final: 0.8075 (m) REVERT: A 636 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 684 GLU cc_start: 0.7779 (tt0) cc_final: 0.7298 (tt0) REVERT: A 740 TRP cc_start: 0.5801 (m100) cc_final: 0.5563 (m-90) REVERT: A 742 PHE cc_start: 0.7939 (t80) cc_final: 0.7588 (t80) REVERT: C 368 LYS cc_start: 0.6900 (tttt) cc_final: 0.6570 (tptm) REVERT: C 416 GLU cc_start: 0.7480 (tp30) cc_final: 0.7136 (tp30) REVERT: C 432 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7152 (tpp-160) REVERT: C 435 TYR cc_start: 0.8790 (m-10) cc_final: 0.8355 (m-80) REVERT: C 442 CYS cc_start: 0.9350 (m) cc_final: 0.9052 (m) REVERT: C 498 GLN cc_start: 0.8991 (mt0) cc_final: 0.8443 (tm-30) REVERT: C 517 PHE cc_start: 0.8908 (t80) cc_final: 0.8594 (t80) REVERT: C 572 MET cc_start: 0.7698 (tpp) cc_final: 0.7238 (tpp) REVERT: C 631 TYR cc_start: 0.7688 (t80) cc_final: 0.7405 (t80) REVERT: C 636 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 644 MET cc_start: 0.9073 (mmm) cc_final: 0.8397 (tpt) REVERT: C 689 ILE cc_start: 0.8755 (pt) cc_final: 0.8470 (pt) REVERT: C 693 SER cc_start: 0.9247 (m) cc_final: 0.8546 (p) REVERT: D 401 TYR cc_start: 0.7189 (m-80) cc_final: 0.6268 (m-80) REVERT: D 426 TRP cc_start: 0.8449 (t-100) cc_final: 0.8165 (t-100) REVERT: D 465 LEU cc_start: 0.8487 (mt) cc_final: 0.8214 (pt) REVERT: D 472 TYR cc_start: 0.8075 (m-80) cc_final: 0.7440 (m-80) REVERT: D 517 PHE cc_start: 0.8909 (t80) cc_final: 0.8550 (t80) REVERT: D 631 TYR cc_start: 0.7501 (t80) cc_final: 0.7105 (t80) REVERT: D 634 CYS cc_start: 0.8679 (m) cc_final: 0.8354 (m) REVERT: D 636 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8309 (mm-30) REVERT: B 363 ARG cc_start: 0.6698 (mtp180) cc_final: 0.6472 (ttm170) REVERT: B 401 TYR cc_start: 0.7204 (m-80) cc_final: 0.6559 (m-80) REVERT: B 431 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8720 (tttt) REVERT: B 435 TYR cc_start: 0.8877 (m-10) cc_final: 0.8590 (m-80) REVERT: B 460 LEU cc_start: 0.8065 (mt) cc_final: 0.7811 (mp) REVERT: B 465 LEU cc_start: 0.8478 (mt) cc_final: 0.8228 (pt) REVERT: B 494 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8986 (mp10) REVERT: B 498 GLN cc_start: 0.8911 (mt0) cc_final: 0.8547 (tm-30) REVERT: B 517 PHE cc_start: 0.8854 (t80) cc_final: 0.8560 (t80) REVERT: B 535 LYS cc_start: 0.8411 (tttt) cc_final: 0.8162 (tppt) REVERT: B 581 MET cc_start: 0.8104 (mmm) cc_final: 0.7799 (mmm) REVERT: B 631 TYR cc_start: 0.7492 (t80) cc_final: 0.7200 (t80) REVERT: B 634 CYS cc_start: 0.8649 (m) cc_final: 0.8367 (m) REVERT: B 636 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 689 ILE cc_start: 0.8793 (pt) cc_final: 0.8485 (pt) REVERT: B 742 PHE cc_start: 0.7974 (t80) cc_final: 0.7657 (t80) outliers start: 8 outliers final: 3 residues processed: 778 average time/residue: 0.1230 time to fit residues: 142.4621 Evaluate side-chains 508 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 505 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 512 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 519 GLN A 560 GLN A 561 GLN C 652 ASN D 354 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN B 519 GLN B 560 GLN B 561 GLN B 652 ASN B 727 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142323 restraints weight = 28136.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146277 restraints weight = 14131.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148665 restraints weight = 9124.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149902 restraints weight = 6987.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.150869 restraints weight = 6027.313| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16362 Z= 0.145 Angle : 0.656 7.993 22153 Z= 0.344 Chirality : 0.040 0.157 2547 Planarity : 0.004 0.040 2724 Dihedral : 4.806 45.787 2176 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.22 % Allowed : 12.93 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1952 helix: 1.53 (0.14), residues: 1204 sheet: 0.44 (0.77), residues: 36 loop : -1.95 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 355 TYR 0.027 0.002 TYR D 463 PHE 0.026 0.002 PHE D 742 TRP 0.018 0.002 TRP C 697 HIS 0.014 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00297 (16362) covalent geometry : angle 0.65578 (22153) hydrogen bonds : bond 0.05034 ( 926) hydrogen bonds : angle 4.49463 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 645 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 TYR cc_start: 0.9354 (t80) cc_final: 0.9079 (t80) REVERT: A 504 LYS cc_start: 0.8519 (mttt) cc_final: 0.8174 (ttmt) REVERT: A 509 ASP cc_start: 0.8633 (t70) cc_final: 0.8327 (p0) REVERT: A 517 PHE cc_start: 0.8679 (t80) cc_final: 0.8236 (t80) REVERT: A 536 GLU cc_start: 0.8914 (mp0) cc_final: 0.8679 (mp0) REVERT: A 557 ARG cc_start: 0.8740 (ptp-170) cc_final: 0.8314 (ptp-170) REVERT: A 585 LEU cc_start: 0.9043 (mm) cc_final: 0.8780 (mm) REVERT: A 644 MET cc_start: 0.9010 (mmm) cc_final: 0.8757 (mmm) REVERT: A 661 ILE cc_start: 0.9442 (mt) cc_final: 0.9075 (tp) REVERT: C 368 LYS cc_start: 0.6836 (tttt) cc_final: 0.6377 (tptm) REVERT: C 382 TYR cc_start: 0.8044 (m-80) cc_final: 0.7728 (m-80) REVERT: C 384 LEU cc_start: 0.8802 (mt) cc_final: 0.8280 (pp) REVERT: C 397 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 416 GLU cc_start: 0.7650 (tp30) cc_final: 0.7167 (tp30) REVERT: C 428 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7644 (mmt180) REVERT: C 435 TYR cc_start: 0.8591 (m-10) cc_final: 0.8280 (m-80) REVERT: C 442 CYS cc_start: 0.9156 (m) cc_final: 0.8920 (m) REVERT: C 465 LEU cc_start: 0.8530 (mt) cc_final: 0.8222 (tp) REVERT: C 474 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8229 (ttm110) REVERT: C 498 GLN cc_start: 0.8919 (mt0) cc_final: 0.8348 (tm-30) REVERT: C 517 PHE cc_start: 0.8751 (t80) cc_final: 0.8328 (t80) REVERT: C 555 TYR cc_start: 0.9122 (m-80) cc_final: 0.8673 (m-80) REVERT: C 636 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8566 (mm-30) REVERT: C 644 MET cc_start: 0.9041 (mmm) cc_final: 0.8547 (tpt) REVERT: C 661 ILE cc_start: 0.9442 (mt) cc_final: 0.9192 (tp) REVERT: C 682 MET cc_start: 0.8136 (mtm) cc_final: 0.7438 (mtp) REVERT: C 691 GLN cc_start: 0.7666 (pm20) cc_final: 0.7034 (pp30) REVERT: C 693 SER cc_start: 0.9113 (m) cc_final: 0.8626 (p) REVERT: D 401 TYR cc_start: 0.7320 (m-80) cc_final: 0.6298 (m-80) REVERT: D 474 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8283 (ptm160) REVERT: D 517 PHE cc_start: 0.8728 (t80) cc_final: 0.8294 (t80) REVERT: D 555 TYR cc_start: 0.9118 (m-80) cc_final: 0.8498 (m-80) REVERT: D 557 ARG cc_start: 0.8846 (ptp-170) cc_final: 0.8467 (ptp-110) REVERT: D 634 CYS cc_start: 0.8366 (m) cc_final: 0.7858 (m) REVERT: D 636 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8549 (mm-30) REVERT: D 661 ILE cc_start: 0.9460 (mt) cc_final: 0.9257 (tp) REVERT: B 258 THR cc_start: 0.8228 (m) cc_final: 0.7960 (p) REVERT: B 363 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6061 (ttm170) REVERT: B 401 TYR cc_start: 0.7359 (m-80) cc_final: 0.6511 (m-80) REVERT: B 474 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8173 (ttm110) REVERT: B 498 GLN cc_start: 0.8810 (mt0) cc_final: 0.8413 (tm-30) REVERT: B 511 TYR cc_start: 0.7685 (m-80) cc_final: 0.7458 (m-80) REVERT: B 517 PHE cc_start: 0.8803 (t80) cc_final: 0.8526 (t80) REVERT: B 555 TYR cc_start: 0.9144 (m-80) cc_final: 0.8669 (m-80) REVERT: B 634 CYS cc_start: 0.8351 (m) cc_final: 0.7930 (m) REVERT: B 636 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 644 MET cc_start: 0.8907 (mmm) cc_final: 0.8321 (mmm) REVERT: B 742 PHE cc_start: 0.8115 (t80) cc_final: 0.7911 (t80) outliers start: 39 outliers final: 29 residues processed: 659 average time/residue: 0.1199 time to fit residues: 119.0377 Evaluate side-chains 533 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 504 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 741 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 185 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 119 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 519 GLN C 727 GLN D 423 GLN D 561 GLN B 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141760 restraints weight = 28664.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145628 restraints weight = 14479.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147972 restraints weight = 9408.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149337 restraints weight = 7235.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150076 restraints weight = 6223.171| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16362 Z= 0.132 Angle : 0.650 13.055 22153 Z= 0.331 Chirality : 0.040 0.204 2547 Planarity : 0.004 0.081 2724 Dihedral : 4.576 34.539 2173 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.08 % Allowed : 16.35 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1952 helix: 1.53 (0.15), residues: 1216 sheet: 0.38 (0.73), residues: 36 loop : -2.18 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 557 TYR 0.026 0.002 TYR B 435 PHE 0.027 0.001 PHE A 742 TRP 0.018 0.001 TRP B 740 HIS 0.005 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00266 (16362) covalent geometry : angle 0.65046 (22153) hydrogen bonds : bond 0.04583 ( 926) hydrogen bonds : angle 4.29778 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 601 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.8353 (tp) cc_final: 0.7974 (tt) REVERT: A 445 MET cc_start: 0.9083 (mmm) cc_final: 0.8721 (mmm) REVERT: A 498 GLN cc_start: 0.9007 (mt0) cc_final: 0.8761 (mt0) REVERT: A 504 LYS cc_start: 0.8554 (mttt) cc_final: 0.8217 (tppt) REVERT: A 557 ARG cc_start: 0.8706 (ptp-170) cc_final: 0.8332 (ptp-170) REVERT: A 572 MET cc_start: 0.8410 (tmm) cc_final: 0.7572 (tpp) REVERT: A 644 MET cc_start: 0.9119 (mmm) cc_final: 0.8888 (mmm) REVERT: A 682 MET cc_start: 0.8206 (mtm) cc_final: 0.7487 (mtp) REVERT: C 368 LYS cc_start: 0.6872 (tttt) cc_final: 0.6264 (tptm) REVERT: C 397 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 428 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7694 (mmt180) REVERT: C 435 TYR cc_start: 0.8638 (m-10) cc_final: 0.8369 (m-80) REVERT: C 442 CYS cc_start: 0.9152 (m) cc_final: 0.8859 (m) REVERT: C 474 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8181 (ttm110) REVERT: C 498 GLN cc_start: 0.8980 (mt0) cc_final: 0.8548 (tm-30) REVERT: C 509 ASP cc_start: 0.8670 (t0) cc_final: 0.8010 (m-30) REVERT: C 517 PHE cc_start: 0.8713 (t80) cc_final: 0.8292 (t80) REVERT: C 555 TYR cc_start: 0.9079 (m-80) cc_final: 0.8586 (m-80) REVERT: C 636 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8500 (mm-30) REVERT: C 644 MET cc_start: 0.9077 (mmm) cc_final: 0.8589 (tpt) REVERT: C 693 SER cc_start: 0.9092 (m) cc_final: 0.8586 (p) REVERT: D 401 TYR cc_start: 0.7449 (m-80) cc_final: 0.6432 (m-80) REVERT: D 426 TRP cc_start: 0.8253 (t-100) cc_final: 0.7967 (t-100) REVERT: D 474 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8287 (ptm160) REVERT: D 517 PHE cc_start: 0.8654 (t80) cc_final: 0.8294 (t80) REVERT: D 555 TYR cc_start: 0.9061 (m-80) cc_final: 0.8390 (m-80) REVERT: D 557 ARG cc_start: 0.8793 (ptp-170) cc_final: 0.8365 (ptp-110) REVERT: D 634 CYS cc_start: 0.8441 (m) cc_final: 0.7973 (m) REVERT: D 697 TRP cc_start: 0.8974 (t60) cc_final: 0.8305 (t60) REVERT: B 366 SER cc_start: 0.6493 (m) cc_final: 0.5803 (m) REVERT: B 401 TYR cc_start: 0.7439 (m-80) cc_final: 0.6572 (m-80) REVERT: B 472 TYR cc_start: 0.7840 (m-80) cc_final: 0.7613 (m-80) REVERT: B 474 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8180 (ttm110) REVERT: B 504 LYS cc_start: 0.8512 (pttm) cc_final: 0.8150 (tppt) REVERT: B 511 TYR cc_start: 0.7827 (m-80) cc_final: 0.7615 (m-80) REVERT: B 517 PHE cc_start: 0.8736 (t80) cc_final: 0.8516 (t80) REVERT: B 555 TYR cc_start: 0.9124 (m-80) cc_final: 0.8450 (m-80) REVERT: B 585 LEU cc_start: 0.8969 (mm) cc_final: 0.8766 (mm) REVERT: B 634 CYS cc_start: 0.8400 (m) cc_final: 0.8019 (m) REVERT: B 636 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8447 (mm-30) REVERT: B 661 ILE cc_start: 0.9445 (mt) cc_final: 0.9108 (tp) REVERT: B 692 GLU cc_start: 0.7903 (mp0) cc_final: 0.7655 (mp0) REVERT: B 742 PHE cc_start: 0.8143 (t80) cc_final: 0.7774 (t80) outliers start: 54 outliers final: 33 residues processed: 620 average time/residue: 0.1116 time to fit residues: 105.7381 Evaluate side-chains 565 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 532 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 14 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 519 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.186608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135236 restraints weight = 28759.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138761 restraints weight = 14866.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140898 restraints weight = 9924.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142061 restraints weight = 7810.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142819 restraints weight = 6811.876| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16362 Z= 0.246 Angle : 0.750 13.035 22153 Z= 0.378 Chirality : 0.044 0.320 2547 Planarity : 0.004 0.058 2724 Dihedral : 4.806 39.418 2173 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.50 % Allowed : 17.21 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1952 helix: 1.22 (0.15), residues: 1216 sheet: 0.25 (0.74), residues: 36 loop : -2.36 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 409 TYR 0.029 0.002 TYR C 441 PHE 0.030 0.002 PHE A 489 TRP 0.018 0.002 TRP D 740 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00547 (16362) covalent geometry : angle 0.75024 (22153) hydrogen bonds : bond 0.04637 ( 926) hydrogen bonds : angle 4.61176 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 515 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8112 (ptt) cc_final: 0.7714 (ptp) REVERT: A 445 MET cc_start: 0.9118 (mmm) cc_final: 0.8818 (mmm) REVERT: A 474 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8364 (ttm110) REVERT: A 504 LYS cc_start: 0.8641 (mttt) cc_final: 0.8277 (tppt) REVERT: A 555 TYR cc_start: 0.9321 (m-80) cc_final: 0.9046 (m-80) REVERT: A 661 ILE cc_start: 0.9494 (mt) cc_final: 0.9100 (tp) REVERT: A 716 MET cc_start: 0.5369 (tpt) cc_final: 0.4981 (ttm) REVERT: C 368 LYS cc_start: 0.6954 (tttt) cc_final: 0.6386 (tptt) REVERT: C 382 TYR cc_start: 0.7956 (m-10) cc_final: 0.7333 (m-10) REVERT: C 397 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8599 (tm-30) REVERT: C 412 MET cc_start: 0.8100 (ptt) cc_final: 0.7492 (ptp) REVERT: C 428 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7700 (mmt180) REVERT: C 435 TYR cc_start: 0.8764 (m-10) cc_final: 0.8513 (m-80) REVERT: C 474 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8284 (ttm110) REVERT: C 498 GLN cc_start: 0.8975 (mt0) cc_final: 0.8410 (tm-30) REVERT: C 517 PHE cc_start: 0.8700 (t80) cc_final: 0.8260 (t80) REVERT: C 555 TYR cc_start: 0.9098 (m-80) cc_final: 0.8707 (m-80) REVERT: C 636 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8455 (mm-30) REVERT: C 644 MET cc_start: 0.8958 (mmm) cc_final: 0.8523 (tpt) REVERT: C 661 ILE cc_start: 0.9493 (mt) cc_final: 0.9242 (tp) REVERT: C 693 SER cc_start: 0.9144 (m) cc_final: 0.8636 (p) REVERT: D 381 LEU cc_start: 0.8363 (mt) cc_final: 0.8143 (tp) REVERT: D 426 TRP cc_start: 0.8171 (t-100) cc_final: 0.7785 (t-100) REVERT: D 472 TYR cc_start: 0.7731 (m-80) cc_final: 0.7293 (m-80) REVERT: D 474 ARG cc_start: 0.8742 (ttp-110) cc_final: 0.8420 (ttm110) REVERT: D 507 PHE cc_start: 0.6172 (m-80) cc_final: 0.5939 (m-80) REVERT: D 517 PHE cc_start: 0.8650 (t80) cc_final: 0.8214 (t80) REVERT: D 555 TYR cc_start: 0.9209 (m-80) cc_final: 0.8730 (m-80) REVERT: D 557 ARG cc_start: 0.8846 (ptp-170) cc_final: 0.7995 (ptp-170) REVERT: D 634 CYS cc_start: 0.8482 (m) cc_final: 0.8085 (m) REVERT: D 661 ILE cc_start: 0.9512 (mt) cc_final: 0.9262 (tp) REVERT: D 716 MET cc_start: 0.5862 (tpt) cc_final: 0.5599 (ttp) REVERT: B 308 MET cc_start: 0.8352 (mmm) cc_final: 0.8121 (mmm) REVERT: B 324 LYS cc_start: 0.5613 (mmmt) cc_final: 0.5369 (mmpt) REVERT: B 474 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8230 (ttp-170) REVERT: B 504 LYS cc_start: 0.8647 (pttm) cc_final: 0.8193 (tppt) REVERT: B 513 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 517 PHE cc_start: 0.8798 (t80) cc_final: 0.8365 (t80) REVERT: B 533 GLN cc_start: 0.8366 (mp10) cc_final: 0.7888 (mp10) REVERT: B 555 TYR cc_start: 0.9223 (m-80) cc_final: 0.8823 (m-80) REVERT: B 630 LEU cc_start: 0.8793 (tp) cc_final: 0.8566 (tt) REVERT: B 634 CYS cc_start: 0.8483 (m) cc_final: 0.7997 (m) REVERT: B 742 PHE cc_start: 0.8083 (t80) cc_final: 0.7621 (t80) outliers start: 79 outliers final: 55 residues processed: 549 average time/residue: 0.1172 time to fit residues: 97.4098 Evaluate side-chains 529 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 474 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 741 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 0.0070 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 163 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 423 GLN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 423 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.192414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141807 restraints weight = 28093.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145681 restraints weight = 14042.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148000 restraints weight = 9127.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149384 restraints weight = 7050.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150091 restraints weight = 6074.454| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16362 Z= 0.127 Angle : 0.655 17.054 22153 Z= 0.331 Chirality : 0.040 0.245 2547 Planarity : 0.004 0.047 2724 Dihedral : 4.464 18.930 2173 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.02 % Allowed : 19.83 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1952 helix: 1.52 (0.15), residues: 1212 sheet: 0.55 (0.78), residues: 36 loop : -2.21 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 409 TYR 0.035 0.002 TYR C 441 PHE 0.030 0.001 PHE C 659 TRP 0.018 0.001 TRP C 426 HIS 0.002 0.000 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00253 (16362) covalent geometry : angle 0.65509 (22153) hydrogen bonds : bond 0.04263 ( 926) hydrogen bonds : angle 4.31111 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 554 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7890 (ptt) cc_final: 0.7526 (ptp) REVERT: A 498 GLN cc_start: 0.8957 (mt0) cc_final: 0.8691 (mp10) REVERT: A 504 LYS cc_start: 0.8646 (mttt) cc_final: 0.8197 (tppt) REVERT: A 517 PHE cc_start: 0.8680 (t80) cc_final: 0.8298 (t80) REVERT: A 555 TYR cc_start: 0.9197 (m-80) cc_final: 0.8870 (m-80) REVERT: A 644 MET cc_start: 0.9105 (mmm) cc_final: 0.8817 (mmm) REVERT: A 656 LYS cc_start: 0.8236 (pttt) cc_final: 0.7895 (pttm) REVERT: A 699 LEU cc_start: 0.9320 (tp) cc_final: 0.9082 (mp) REVERT: A 716 MET cc_start: 0.5005 (tpt) cc_final: 0.4647 (ttm) REVERT: C 368 LYS cc_start: 0.6826 (tttt) cc_final: 0.6226 (tptt) REVERT: C 381 LEU cc_start: 0.7926 (tp) cc_final: 0.7472 (mm) REVERT: C 409 ARG cc_start: 0.6658 (ptt-90) cc_final: 0.6214 (ptp90) REVERT: C 412 MET cc_start: 0.8044 (ptt) cc_final: 0.7454 (ptp) REVERT: C 428 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7567 (mmt180) REVERT: C 474 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8236 (ttm110) REVERT: C 498 GLN cc_start: 0.8958 (mt0) cc_final: 0.8426 (tm-30) REVERT: C 509 ASP cc_start: 0.8730 (t0) cc_final: 0.8156 (m-30) REVERT: C 517 PHE cc_start: 0.8584 (t80) cc_final: 0.8232 (t80) REVERT: C 555 TYR cc_start: 0.8860 (m-80) cc_final: 0.8549 (m-80) REVERT: C 572 MET cc_start: 0.8488 (tmm) cc_final: 0.7520 (tpp) REVERT: C 682 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7219 (mtm) REVERT: C 693 SER cc_start: 0.9117 (m) cc_final: 0.8581 (p) REVERT: D 381 LEU cc_start: 0.8316 (mt) cc_final: 0.7567 (tt) REVERT: D 426 TRP cc_start: 0.8215 (t-100) cc_final: 0.7948 (t-100) REVERT: D 472 TYR cc_start: 0.7678 (m-80) cc_final: 0.7171 (m-80) REVERT: D 474 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8383 (ttm110) REVERT: D 513 GLU cc_start: 0.8061 (mp0) cc_final: 0.7725 (mp0) REVERT: D 555 TYR cc_start: 0.8933 (m-80) cc_final: 0.8618 (m-80) REVERT: D 557 ARG cc_start: 0.8791 (ptp-170) cc_final: 0.8006 (ptp-170) REVERT: D 634 CYS cc_start: 0.8426 (m) cc_final: 0.7969 (m) REVERT: D 656 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7557 (tttm) REVERT: D 716 MET cc_start: 0.6090 (tpt) cc_final: 0.5738 (ttp) REVERT: B 366 SER cc_start: 0.6440 (m) cc_final: 0.6223 (m) REVERT: B 412 MET cc_start: 0.8032 (ptt) cc_final: 0.7288 (ptp) REVERT: B 445 MET cc_start: 0.9236 (mmm) cc_final: 0.8958 (mmm) REVERT: B 504 LYS cc_start: 0.8590 (pttm) cc_final: 0.8211 (tppt) REVERT: B 511 TYR cc_start: 0.7986 (m-80) cc_final: 0.7659 (m-80) REVERT: B 517 PHE cc_start: 0.8695 (t80) cc_final: 0.8119 (t80) REVERT: B 533 GLN cc_start: 0.8284 (mp10) cc_final: 0.7969 (mp10) REVERT: B 555 TYR cc_start: 0.8949 (m-80) cc_final: 0.8566 (m-80) REVERT: B 634 CYS cc_start: 0.8422 (m) cc_final: 0.8010 (m) REVERT: B 644 MET cc_start: 0.9057 (mmm) cc_final: 0.8518 (tpt) REVERT: B 661 ILE cc_start: 0.9415 (mt) cc_final: 0.9131 (tp) REVERT: B 742 PHE cc_start: 0.8079 (t80) cc_final: 0.7525 (t80) outliers start: 53 outliers final: 36 residues processed: 570 average time/residue: 0.1172 time to fit residues: 101.2171 Evaluate side-chains 529 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 491 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 741 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 378 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.139998 restraints weight = 28780.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143761 restraints weight = 14548.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146043 restraints weight = 9502.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147264 restraints weight = 7378.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148048 restraints weight = 6443.432| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16362 Z= 0.141 Angle : 0.671 16.954 22153 Z= 0.336 Chirality : 0.042 0.323 2547 Planarity : 0.004 0.048 2724 Dihedral : 4.425 22.576 2172 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.25 % Allowed : 20.74 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1952 helix: 1.29 (0.15), residues: 1240 sheet: 0.59 (0.79), residues: 36 loop : -2.42 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 557 TYR 0.038 0.002 TYR B 309 PHE 0.029 0.002 PHE B 489 TRP 0.018 0.001 TRP C 426 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00308 (16362) covalent geometry : angle 0.67083 (22153) hydrogen bonds : bond 0.04198 ( 926) hydrogen bonds : angle 4.36862 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 515 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7831 (ptt) cc_final: 0.7448 (ptp) REVERT: A 421 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 474 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8408 (ttm110) REVERT: A 504 LYS cc_start: 0.8579 (mttt) cc_final: 0.8230 (tppt) REVERT: A 517 PHE cc_start: 0.8720 (t80) cc_final: 0.8335 (t80) REVERT: A 555 TYR cc_start: 0.9196 (m-80) cc_final: 0.8977 (m-80) REVERT: A 656 LYS cc_start: 0.8219 (pttt) cc_final: 0.7921 (pttm) REVERT: A 661 ILE cc_start: 0.9434 (mt) cc_final: 0.9138 (tp) REVERT: A 699 LEU cc_start: 0.9327 (tp) cc_final: 0.9107 (mp) REVERT: A 701 ARG cc_start: 0.8666 (mtp85) cc_final: 0.7633 (ttm-80) REVERT: A 716 MET cc_start: 0.5105 (tpt) cc_final: 0.4756 (ttm) REVERT: A 728 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8328 (t) REVERT: C 368 LYS cc_start: 0.6896 (tttt) cc_final: 0.6280 (tptt) REVERT: C 409 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6084 (ptp-170) REVERT: C 412 MET cc_start: 0.7973 (ptt) cc_final: 0.7431 (ptp) REVERT: C 428 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7755 (mmt180) REVERT: C 431 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8245 (ttpt) REVERT: C 474 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8246 (ttm110) REVERT: C 509 ASP cc_start: 0.8614 (t0) cc_final: 0.7859 (m-30) REVERT: C 517 PHE cc_start: 0.8631 (t80) cc_final: 0.8366 (t80) REVERT: C 572 MET cc_start: 0.8546 (tmm) cc_final: 0.7624 (tpp) REVERT: C 682 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7317 (mtm) REVERT: C 693 SER cc_start: 0.9066 (m) cc_final: 0.8553 (p) REVERT: C 742 PHE cc_start: 0.7869 (t80) cc_final: 0.7575 (t80) REVERT: D 381 LEU cc_start: 0.8372 (mt) cc_final: 0.8138 (tp) REVERT: D 426 TRP cc_start: 0.8196 (t-100) cc_final: 0.7976 (t-100) REVERT: D 442 CYS cc_start: 0.8944 (m) cc_final: 0.8673 (m) REVERT: D 472 TYR cc_start: 0.7640 (m-80) cc_final: 0.7118 (m-80) REVERT: D 513 GLU cc_start: 0.8054 (mp0) cc_final: 0.7729 (mp0) REVERT: D 517 PHE cc_start: 0.8513 (t80) cc_final: 0.8097 (t80) REVERT: D 634 CYS cc_start: 0.8465 (m) cc_final: 0.8038 (m) REVERT: D 716 MET cc_start: 0.6124 (tpt) cc_final: 0.5766 (ttp) REVERT: B 412 MET cc_start: 0.8046 (ptt) cc_final: 0.7272 (ptp) REVERT: B 442 CYS cc_start: 0.8904 (m) cc_final: 0.8703 (m) REVERT: B 445 MET cc_start: 0.9195 (mmm) cc_final: 0.8971 (mmm) REVERT: B 504 LYS cc_start: 0.8535 (pttm) cc_final: 0.8193 (tppt) REVERT: B 511 TYR cc_start: 0.8041 (m-80) cc_final: 0.7709 (m-80) REVERT: B 634 CYS cc_start: 0.8428 (m) cc_final: 0.8036 (m) REVERT: B 644 MET cc_start: 0.8900 (mmm) cc_final: 0.8670 (tpp) REVERT: B 661 ILE cc_start: 0.9450 (mt) cc_final: 0.9162 (tp) REVERT: B 742 PHE cc_start: 0.8023 (t80) cc_final: 0.7528 (t80) outliers start: 57 outliers final: 38 residues processed: 537 average time/residue: 0.1203 time to fit residues: 97.2779 Evaluate side-chains 520 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 479 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** B 297 ASN ** 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 = 0.4321 r_free = 0.4321 target = 0.192664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141616 restraints weight = 28418.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145421 restraints weight = 14194.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147663 restraints weight = 9270.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148943 restraints weight = 7212.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149673 restraints weight = 6245.786| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16362 Z= 0.132 Angle : 0.676 18.400 22153 Z= 0.337 Chirality : 0.042 0.338 2547 Planarity : 0.004 0.044 2724 Dihedral : 4.400 22.793 2172 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.74 % Allowed : 21.48 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1952 helix: 1.23 (0.15), residues: 1240 sheet: 0.67 (0.79), residues: 36 loop : -2.44 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 557 TYR 0.033 0.002 TYR B 441 PHE 0.034 0.001 PHE D 507 TRP 0.020 0.001 TRP C 426 HIS 0.002 0.000 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00285 (16362) covalent geometry : angle 0.67610 (22153) hydrogen bonds : bond 0.04188 ( 926) hydrogen bonds : angle 4.35497 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 505 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7767 (ptt) cc_final: 0.7322 (ptp) REVERT: A 474 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8381 (ttm110) REVERT: A 504 LYS cc_start: 0.8535 (mttt) cc_final: 0.8220 (tppt) REVERT: A 517 PHE cc_start: 0.8731 (t80) cc_final: 0.8142 (t80) REVERT: A 656 LYS cc_start: 0.8212 (pttt) cc_final: 0.7882 (pttm) REVERT: A 661 ILE cc_start: 0.9446 (mt) cc_final: 0.9186 (tp) REVERT: A 677 MET cc_start: 0.7660 (mmm) cc_final: 0.7324 (mmm) REVERT: A 699 LEU cc_start: 0.9300 (tp) cc_final: 0.9097 (mp) REVERT: A 701 ARG cc_start: 0.8686 (mtp85) cc_final: 0.7591 (ttm-80) REVERT: A 716 MET cc_start: 0.5469 (tpt) cc_final: 0.5071 (ttm) REVERT: C 368 LYS cc_start: 0.6871 (tttt) cc_final: 0.6277 (tptt) REVERT: C 381 LEU cc_start: 0.7644 (tp) cc_final: 0.7276 (tp) REVERT: C 409 ARG cc_start: 0.6676 (ptt-90) cc_final: 0.6140 (ptt-90) REVERT: C 412 MET cc_start: 0.7789 (ptt) cc_final: 0.7343 (ptp) REVERT: C 428 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7702 (mmt180) REVERT: C 474 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8207 (ttm110) REVERT: C 509 ASP cc_start: 0.8545 (t0) cc_final: 0.7966 (m-30) REVERT: C 517 PHE cc_start: 0.8622 (t80) cc_final: 0.8275 (t80) REVERT: C 682 MET cc_start: 0.8293 (ttm) cc_final: 0.8054 (ttm) REVERT: C 716 MET cc_start: 0.6082 (ttt) cc_final: 0.5592 (ttm) REVERT: C 742 PHE cc_start: 0.7963 (t80) cc_final: 0.7504 (t80) REVERT: D 311 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8485 (mt-10) REVERT: D 381 LEU cc_start: 0.8409 (mt) cc_final: 0.8198 (tp) REVERT: D 426 TRP cc_start: 0.8176 (t-100) cc_final: 0.7972 (t-100) REVERT: D 442 CYS cc_start: 0.8909 (m) cc_final: 0.8638 (m) REVERT: D 472 TYR cc_start: 0.7649 (m-80) cc_final: 0.7140 (m-80) REVERT: D 513 GLU cc_start: 0.7970 (mp0) cc_final: 0.7648 (mp0) REVERT: D 517 PHE cc_start: 0.8501 (t80) cc_final: 0.8215 (t80) REVERT: D 634 CYS cc_start: 0.8474 (m) cc_final: 0.8028 (m) REVERT: D 716 MET cc_start: 0.6127 (tpt) cc_final: 0.5736 (ttp) REVERT: B 409 ARG cc_start: 0.6101 (ptp90) cc_final: 0.5773 (ptp90) REVERT: B 412 MET cc_start: 0.8087 (ptt) cc_final: 0.7416 (ptp) REVERT: B 426 TRP cc_start: 0.8059 (t-100) cc_final: 0.7352 (t-100) REVERT: B 442 CYS cc_start: 0.8902 (m) cc_final: 0.8655 (m) REVERT: B 444 TYR cc_start: 0.8911 (t80) cc_final: 0.8701 (t80) REVERT: B 504 LYS cc_start: 0.8565 (pttm) cc_final: 0.8214 (tppt) REVERT: B 511 TYR cc_start: 0.8005 (m-80) cc_final: 0.7695 (m-80) REVERT: B 557 ARG cc_start: 0.8831 (ptp-170) cc_final: 0.7874 (ptp-170) REVERT: B 634 CYS cc_start: 0.8468 (m) cc_final: 0.8078 (m) REVERT: B 644 MET cc_start: 0.8901 (mmm) cc_final: 0.8638 (tpp) REVERT: B 701 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7358 (ttm-80) REVERT: B 742 PHE cc_start: 0.8083 (t80) cc_final: 0.7606 (t80) outliers start: 48 outliers final: 40 residues processed: 524 average time/residue: 0.1218 time to fit residues: 96.3797 Evaluate side-chains 526 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 486 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 33 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 GLN B 297 ASN B 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.191686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140763 restraints weight = 28575.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144513 restraints weight = 14481.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146770 restraints weight = 9499.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148096 restraints weight = 7366.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148781 restraints weight = 6362.207| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16362 Z= 0.150 Angle : 0.687 17.345 22153 Z= 0.344 Chirality : 0.042 0.318 2547 Planarity : 0.004 0.057 2724 Dihedral : 4.406 23.103 2172 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.08 % Allowed : 21.48 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1952 helix: 1.16 (0.15), residues: 1236 sheet: 0.77 (0.79), residues: 36 loop : -2.46 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 557 TYR 0.034 0.002 TYR B 441 PHE 0.034 0.002 PHE C 659 TRP 0.015 0.001 TRP D 549 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00334 (16362) covalent geometry : angle 0.68699 (22153) hydrogen bonds : bond 0.04187 ( 926) hydrogen bonds : angle 4.42507 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 500 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8379 (ttm110) REVERT: A 504 LYS cc_start: 0.8550 (mttt) cc_final: 0.8257 (tppt) REVERT: A 656 LYS cc_start: 0.8232 (pttt) cc_final: 0.7883 (pttm) REVERT: A 716 MET cc_start: 0.5639 (tpt) cc_final: 0.5232 (ttm) REVERT: C 368 LYS cc_start: 0.6966 (tttt) cc_final: 0.6345 (tptt) REVERT: C 381 LEU cc_start: 0.7709 (tp) cc_final: 0.7350 (tp) REVERT: C 409 ARG cc_start: 0.6550 (ptt-90) cc_final: 0.6043 (ptt-90) REVERT: C 412 MET cc_start: 0.7814 (ptt) cc_final: 0.7335 (ptp) REVERT: C 428 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7656 (mmt180) REVERT: C 474 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8235 (ttm110) REVERT: C 498 GLN cc_start: 0.8958 (mt0) cc_final: 0.8418 (tm-30) REVERT: C 509 ASP cc_start: 0.8536 (t0) cc_final: 0.7933 (m-30) REVERT: C 517 PHE cc_start: 0.8613 (t80) cc_final: 0.8357 (t80) REVERT: C 716 MET cc_start: 0.6196 (ttt) cc_final: 0.5698 (ttm) REVERT: C 742 PHE cc_start: 0.7968 (t80) cc_final: 0.7502 (t80) REVERT: D 381 LEU cc_start: 0.8419 (mt) cc_final: 0.8208 (tp) REVERT: D 426 TRP cc_start: 0.8123 (t-100) cc_final: 0.7831 (t-100) REVERT: D 442 CYS cc_start: 0.8973 (m) cc_final: 0.8761 (m) REVERT: D 472 TYR cc_start: 0.7646 (m-80) cc_final: 0.7208 (m-80) REVERT: D 513 GLU cc_start: 0.8023 (mp0) cc_final: 0.7716 (mp0) REVERT: D 524 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 634 CYS cc_start: 0.8480 (m) cc_final: 0.8044 (m) REVERT: D 716 MET cc_start: 0.6072 (tpt) cc_final: 0.5781 (ttp) REVERT: B 409 ARG cc_start: 0.6092 (ptp90) cc_final: 0.5728 (ptp90) REVERT: B 412 MET cc_start: 0.8163 (ptt) cc_final: 0.7518 (ptp) REVERT: B 426 TRP cc_start: 0.8049 (t-100) cc_final: 0.7263 (t-100) REVERT: B 504 LYS cc_start: 0.8569 (pttm) cc_final: 0.8213 (tppt) REVERT: B 511 TYR cc_start: 0.8027 (m-80) cc_final: 0.7793 (m-80) REVERT: B 513 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 634 CYS cc_start: 0.8481 (m) cc_final: 0.8158 (m) REVERT: B 644 MET cc_start: 0.8891 (mmm) cc_final: 0.8635 (tpp) REVERT: B 661 ILE cc_start: 0.9409 (mt) cc_final: 0.9158 (tp) REVERT: B 701 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7312 (ttm-80) REVERT: B 742 PHE cc_start: 0.8072 (t80) cc_final: 0.7626 (t80) outliers start: 54 outliers final: 48 residues processed: 521 average time/residue: 0.1211 time to fit residues: 94.2874 Evaluate side-chains 528 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.0040 chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 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 = 0.4310 r_free = 0.4310 target = 0.191731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140922 restraints weight = 28466.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144694 restraints weight = 14377.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146919 restraints weight = 9413.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148267 restraints weight = 7320.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148887 restraints weight = 6322.205| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16362 Z= 0.149 Angle : 0.704 17.467 22153 Z= 0.354 Chirality : 0.042 0.292 2547 Planarity : 0.004 0.069 2724 Dihedral : 4.463 23.022 2172 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.19 % Allowed : 22.34 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1952 helix: 1.08 (0.15), residues: 1236 sheet: 0.82 (0.80), residues: 36 loop : -2.49 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 409 TYR 0.036 0.002 TYR B 441 PHE 0.029 0.001 PHE A 659 TRP 0.023 0.002 TRP D 549 HIS 0.002 0.000 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00334 (16362) covalent geometry : angle 0.70358 (22153) hydrogen bonds : bond 0.04236 ( 926) hydrogen bonds : angle 4.49497 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 493 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.5722 (t80) cc_final: 0.5229 (t80) REVERT: A 412 MET cc_start: 0.7718 (ptt) cc_final: 0.7090 (ptp) REVERT: A 474 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8374 (ttm110) REVERT: A 504 LYS cc_start: 0.8555 (mttt) cc_final: 0.8303 (tppt) REVERT: A 560 GLN cc_start: 0.8502 (tp40) cc_final: 0.8132 (mp10) REVERT: A 656 LYS cc_start: 0.8242 (pttt) cc_final: 0.7860 (pttm) REVERT: A 673 LEU cc_start: 0.8644 (tt) cc_final: 0.8384 (tt) REVERT: A 677 MET cc_start: 0.8308 (mmm) cc_final: 0.7845 (mmm) REVERT: A 682 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: A 701 ARG cc_start: 0.8654 (mtp85) cc_final: 0.7833 (ttm-80) REVERT: A 716 MET cc_start: 0.5765 (tpt) cc_final: 0.5304 (ttm) REVERT: A 728 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 368 LYS cc_start: 0.6972 (tttt) cc_final: 0.6349 (tptt) REVERT: C 381 LEU cc_start: 0.7697 (tp) cc_final: 0.7349 (tp) REVERT: C 428 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7642 (mmt180) REVERT: C 474 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8246 (ttm110) REVERT: C 498 GLN cc_start: 0.9025 (mt0) cc_final: 0.8436 (tm-30) REVERT: C 509 ASP cc_start: 0.8527 (t0) cc_final: 0.7940 (m-30) REVERT: C 517 PHE cc_start: 0.8630 (t80) cc_final: 0.8334 (t80) REVERT: C 716 MET cc_start: 0.6188 (ttt) cc_final: 0.5653 (ttm) REVERT: C 742 PHE cc_start: 0.7960 (t80) cc_final: 0.7492 (t80) REVERT: D 381 LEU cc_start: 0.8410 (mt) cc_final: 0.8188 (tp) REVERT: D 472 TYR cc_start: 0.7644 (m-80) cc_final: 0.7189 (m-80) REVERT: D 513 GLU cc_start: 0.8047 (mp0) cc_final: 0.7737 (mp0) REVERT: D 524 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8829 (mm) REVERT: D 634 CYS cc_start: 0.8452 (m) cc_final: 0.8029 (m) REVERT: D 716 MET cc_start: 0.6056 (tpt) cc_final: 0.5702 (ttp) REVERT: B 409 ARG cc_start: 0.6097 (ptp90) cc_final: 0.5724 (ptp90) REVERT: B 412 MET cc_start: 0.8255 (ptt) cc_final: 0.7711 (ptp) REVERT: B 426 TRP cc_start: 0.8122 (t-100) cc_final: 0.7374 (t-100) REVERT: B 504 LYS cc_start: 0.8496 (pttm) cc_final: 0.8221 (tppt) REVERT: B 511 TYR cc_start: 0.8060 (m-80) cc_final: 0.7856 (m-80) REVERT: B 513 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 517 PHE cc_start: 0.8622 (t80) cc_final: 0.8136 (t80) REVERT: B 634 CYS cc_start: 0.8511 (m) cc_final: 0.8132 (m) REVERT: B 644 MET cc_start: 0.8803 (mmm) cc_final: 0.8550 (tpp) REVERT: B 661 ILE cc_start: 0.9413 (mt) cc_final: 0.9190 (tp) REVERT: B 701 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7247 (ttm-80) REVERT: B 742 PHE cc_start: 0.8075 (t80) cc_final: 0.7638 (t80) outliers start: 56 outliers final: 45 residues processed: 518 average time/residue: 0.1198 time to fit residues: 93.4395 Evaluate side-chains 529 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 148 optimal weight: 0.0020 chunk 85 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 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 = 0.4330 r_free = 0.4330 target = 0.193477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144280 restraints weight = 28761.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148047 restraints weight = 14548.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150327 restraints weight = 8615.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150535 restraints weight = 6952.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150618 restraints weight = 6747.145| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16362 Z= 0.136 Angle : 0.720 17.730 22153 Z= 0.359 Chirality : 0.042 0.287 2547 Planarity : 0.004 0.063 2724 Dihedral : 4.421 22.772 2172 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.68 % Allowed : 23.65 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1952 helix: 1.05 (0.15), residues: 1236 sheet: 0.82 (0.80), residues: 36 loop : -2.48 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 409 TYR 0.036 0.002 TYR C 435 PHE 0.030 0.001 PHE A 659 TRP 0.025 0.002 TRP D 549 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00298 (16362) covalent geometry : angle 0.71981 (22153) hydrogen bonds : bond 0.04194 ( 926) hydrogen bonds : angle 4.47910 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 514 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.5866 (t80) cc_final: 0.5307 (t80) REVERT: A 412 MET cc_start: 0.7743 (ptt) cc_final: 0.7074 (ptp) REVERT: A 474 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8357 (ttm110) REVERT: A 498 GLN cc_start: 0.8972 (mt0) cc_final: 0.8670 (mp10) REVERT: A 504 LYS cc_start: 0.8572 (mttt) cc_final: 0.8298 (tppt) REVERT: A 560 GLN cc_start: 0.8489 (tp40) cc_final: 0.8136 (mp10) REVERT: A 572 MET cc_start: 0.8551 (tmm) cc_final: 0.7674 (tpp) REVERT: A 656 LYS cc_start: 0.8108 (pttt) cc_final: 0.7777 (pttm) REVERT: A 673 LEU cc_start: 0.8510 (tt) cc_final: 0.8278 (tt) REVERT: A 677 MET cc_start: 0.8124 (mmm) cc_final: 0.7542 (mmm) REVERT: A 701 ARG cc_start: 0.8670 (mtp85) cc_final: 0.7842 (ttm-80) REVERT: A 716 MET cc_start: 0.5634 (tpt) cc_final: 0.5207 (ttm) REVERT: C 368 LYS cc_start: 0.6868 (tttt) cc_final: 0.6291 (tptt) REVERT: C 381 LEU cc_start: 0.7664 (tp) cc_final: 0.7335 (tp) REVERT: C 428 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7650 (mmt180) REVERT: C 474 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8201 (ttm110) REVERT: C 498 GLN cc_start: 0.8974 (mt0) cc_final: 0.8427 (tm-30) REVERT: C 509 ASP cc_start: 0.8527 (t0) cc_final: 0.7992 (m-30) REVERT: C 636 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 716 MET cc_start: 0.6305 (ttt) cc_final: 0.6094 (ttt) REVERT: C 742 PHE cc_start: 0.8114 (t80) cc_final: 0.7659 (t80) REVERT: D 472 TYR cc_start: 0.7586 (m-80) cc_final: 0.7132 (m-80) REVERT: D 513 GLU cc_start: 0.8000 (mp0) cc_final: 0.7681 (mp0) REVERT: D 634 CYS cc_start: 0.8497 (m) cc_final: 0.8072 (m) REVERT: D 716 MET cc_start: 0.5967 (tpt) cc_final: 0.5537 (ttm) REVERT: B 381 LEU cc_start: 0.7803 (tp) cc_final: 0.7495 (tt) REVERT: B 409 ARG cc_start: 0.6069 (ptp90) cc_final: 0.5695 (ptp90) REVERT: B 412 MET cc_start: 0.8257 (ptt) cc_final: 0.7673 (ptp) REVERT: B 426 TRP cc_start: 0.8116 (t-100) cc_final: 0.7371 (t-100) REVERT: B 504 LYS cc_start: 0.8544 (pttm) cc_final: 0.8266 (tppt) REVERT: B 511 TYR cc_start: 0.8104 (m-80) cc_final: 0.7722 (m-80) REVERT: B 513 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 524 LEU cc_start: 0.9286 (mm) cc_final: 0.8951 (mm) REVERT: B 634 CYS cc_start: 0.8471 (m) cc_final: 0.8091 (m) REVERT: B 644 MET cc_start: 0.8790 (mmm) cc_final: 0.8525 (tpp) REVERT: B 656 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7892 (tmmt) REVERT: B 701 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7223 (ttm-80) REVERT: B 742 PHE cc_start: 0.8278 (t80) cc_final: 0.7903 (t80) outliers start: 47 outliers final: 39 residues processed: 532 average time/residue: 0.1253 time to fit residues: 99.9372 Evaluate side-chains 524 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 484 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 113 optimal weight: 0.0870 chunk 98 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.194781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143324 restraints weight = 28322.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147142 restraints weight = 14174.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149395 restraints weight = 9259.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150615 restraints weight = 7193.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151306 restraints weight = 6255.563| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16362 Z= 0.137 Angle : 0.732 17.877 22153 Z= 0.366 Chirality : 0.043 0.331 2547 Planarity : 0.004 0.056 2724 Dihedral : 4.409 24.327 2172 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.34 % Allowed : 24.22 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1952 helix: 0.97 (0.15), residues: 1236 sheet: 0.71 (0.81), residues: 36 loop : -2.45 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 557 TYR 0.045 0.002 TYR C 435 PHE 0.027 0.001 PHE A 489 TRP 0.025 0.002 TRP D 549 HIS 0.002 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00300 (16362) covalent geometry : angle 0.73208 (22153) hydrogen bonds : bond 0.04201 ( 926) hydrogen bonds : angle 4.52617 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.74 seconds wall clock time: 55 minutes 10.06 seconds (3310.06 seconds total)