Starting phenix.real_space_refine on Sun Aug 24 01:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpd_23478/08_2025/7lpd_23478.map" } resolution = 3.55 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= 0.005 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 84 5.16 5 C 10312 2.51 5 N 2404 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15564 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3733 Classifications: {'peptide': 497} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 88} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 484} Chain breaks: 3 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 10, 'ASN:plan1': 6, 'GLN:plan1': 4, 'ASP:plan': 11, 'TYR:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 196 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'4DY': 1, '6OU': 4, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'LBN:plan-3': 2, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 94 Unusual residues: {'4DY': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'6OU:plan-1': 2, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 94 Unusual residues: {'4DY': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'6OU:plan-1': 2, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'6OU:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA D 204 " occ=0.50 Time building chain proxies: 3.06, per 1000 atoms: 0.20 Number of scatterers: 15564 At special positions: 0 Unit cell: (110.136, 109.077, 105.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 16 15.00 O 2748 8.00 N 2404 7.00 C 10312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 479.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 72.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.665A pdb=" N VAL A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.538A pdb=" N CYS A 362 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.559A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.513A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.673A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 removed outlier: 4.020A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 4.044A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.763A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.744A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 4.188A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.657A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 690 Processing helix chain 'A' and resid 692 through 711 removed outlier: 3.961A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 720 Processing helix chain 'A' and resid 749 through 752 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 removed outlier: 3.665A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.538A pdb=" N CYS B 362 " --> pdb=" O GLU B 359 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 363' Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.559A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.513A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.673A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 removed outlier: 4.020A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.044A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 560 through 575 removed outlier: 3.763A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.745A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 4.188A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.657A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 690 Processing helix chain 'B' and resid 692 through 711 removed outlier: 3.961A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 720 Processing helix chain 'B' and resid 749 through 752 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.665A pdb=" N VAL C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.538A pdb=" N CYS C 362 " --> pdb=" O GLU C 359 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 363' Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.559A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.513A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.673A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 removed outlier: 4.021A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 4.044A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.763A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.745A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 4.188A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.658A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 690 Processing helix chain 'C' and resid 692 through 711 removed outlier: 3.961A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 720 Processing helix chain 'C' and resid 749 through 752 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 removed outlier: 3.664A pdb=" N VAL D 264 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.538A pdb=" N CYS D 362 " --> pdb=" O GLU D 359 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG D 363 " --> pdb=" O PRO D 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 363' Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.559A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.513A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.673A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 removed outlier: 4.020A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 4.044A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 560 through 575 removed outlier: 3.763A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.745A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 4.189A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.657A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 690 Processing helix chain 'D' and resid 692 through 711 removed outlier: 3.962A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 720 Processing helix chain 'D' and resid 749 through 752 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372 removed outlier: 6.725A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 372 removed outlier: 6.725A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 368 through 372 removed outlier: 6.725A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 368 through 372 removed outlier: 6.725A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2943 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: 1.67 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2316 1.30 - 1.43: 4490 1.43 - 1.56: 8859 1.56 - 1.70: 67 1.70 - 1.83: 168 Bond restraints: 15900 Sorted by residual: bond pdb=" O22 6OU A 902 " pdb=" P23 6OU A 902 " ideal model delta sigma weight residual 1.643 1.769 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" O22 6OU D 902 " pdb=" P23 6OU D 902 " ideal model delta sigma weight residual 1.643 1.769 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" O22 6OU B 902 " pdb=" P23 6OU B 902 " ideal model delta sigma weight residual 1.643 1.769 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" O22 6OU C 902 " pdb=" P23 6OU C 902 " ideal model delta sigma weight residual 1.643 1.769 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" O22 6OU C 903 " pdb=" P23 6OU C 903 " ideal model delta sigma weight residual 1.643 1.767 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 15895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 20849 2.71 - 5.41: 589 5.41 - 8.12: 74 8.12 - 10.83: 28 10.83 - 13.53: 16 Bond angle restraints: 21556 Sorted by residual: angle pdb=" N MET D 677 " pdb=" CA MET D 677 " pdb=" C MET D 677 " ideal model delta sigma weight residual 111.69 100.99 10.70 1.23e+00 6.61e-01 7.57e+01 angle pdb=" N MET B 677 " pdb=" CA MET B 677 " pdb=" C MET B 677 " ideal model delta sigma weight residual 111.69 101.00 10.69 1.23e+00 6.61e-01 7.55e+01 angle pdb=" N MET A 677 " pdb=" CA MET A 677 " pdb=" C MET A 677 " ideal model delta sigma weight residual 111.69 101.00 10.69 1.23e+00 6.61e-01 7.55e+01 angle pdb=" N MET C 677 " pdb=" CA MET C 677 " pdb=" C MET C 677 " ideal model delta sigma weight residual 111.69 101.03 10.66 1.23e+00 6.61e-01 7.51e+01 angle pdb=" C ARG C 557 " pdb=" N GLY C 558 " pdb=" CA GLY C 558 " ideal model delta sigma weight residual 120.00 127.43 -7.43 1.10e+00 8.26e-01 4.56e+01 ... (remaining 21551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8988 35.47 - 70.94: 248 70.94 - 106.41: 36 106.41 - 141.88: 12 141.88 - 177.35: 36 Dihedral angle restraints: 9320 sinusoidal: 3468 harmonic: 5852 Sorted by residual: dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 44.48 48.52 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual 93.00 44.52 48.48 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 44.53 48.47 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 9317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 2456 0.351 - 0.701: 16 0.701 - 1.052: 0 1.052 - 1.402: 0 1.402 - 1.753: 4 Chirality restraints: 2476 Sorted by residual: chirality pdb=" CG LEU D 706 " pdb=" CB LEU D 706 " pdb=" CD1 LEU D 706 " pdb=" CD2 LEU D 706 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.68e+01 chirality pdb=" CG LEU B 706 " pdb=" CB LEU B 706 " pdb=" CD1 LEU B 706 " pdb=" CD2 LEU B 706 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" CG LEU A 706 " pdb=" CB LEU A 706 " pdb=" CD1 LEU A 706 " pdb=" CD2 LEU A 706 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.65e+01 ... (remaining 2473 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 557 " -0.020 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ARG B 557 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG B 557 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 558 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 557 " -0.020 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ARG C 557 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG C 557 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY C 558 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 557 " 0.020 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ARG A 557 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 557 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY A 558 " 0.021 2.00e-02 2.50e+03 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 68 2.55 - 3.14: 12912 3.14 - 3.73: 23783 3.73 - 4.31: 31628 4.31 - 4.90: 55251 Nonbonded interactions: 123642 Sorted by model distance: nonbonded pdb=" CE MET A 572 " pdb=" SD MET D 677 " model vdw 1.966 3.820 nonbonded pdb=" SD MET B 677 " pdb=" CE MET C 572 " model vdw 1.967 3.820 nonbonded pdb=" SD MET C 677 " pdb=" CE MET D 572 " model vdw 1.970 3.820 nonbonded pdb=" SD MET A 677 " pdb=" CE MET B 572 " model vdw 1.973 3.820 nonbonded pdb=" SD MET A 572 " pdb=" CE MET D 677 " model vdw 2.066 3.820 ... (remaining 123637 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 204 through 902) selection = (chain 'B' and resid 204 through 902) selection = (chain 'C' and resid 204 through 902) selection = (chain 'D' and resid 204 through 902) } 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=0.50 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: 1.610 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.010 0.126 15904 Z= 0.511 Angle : 1.089 13.533 21564 Z= 0.541 Chirality : 0.090 1.753 2476 Planarity : 0.005 0.057 2620 Dihedral : 21.333 177.345 5532 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.19), residues: 1956 helix: 0.30 (0.14), residues: 1252 sheet: -3.40 (0.40), residues: 116 loop : -0.37 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 420 TYR 0.021 0.002 TYR C 565 PHE 0.018 0.002 PHE D 659 TRP 0.012 0.001 TRP A 697 HIS 0.008 0.002 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00980 (15900) covalent geometry : angle 1.08812 (21556) SS BOND : bond 0.00745 ( 4) SS BOND : angle 1.95249 ( 8) hydrogen bonds : bond 0.14396 ( 1013) hydrogen bonds : angle 6.04468 ( 2943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.383 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: A 496 PHE cc_start: 0.7135 (t80) cc_final: 0.6853 (m-80) REVERT: A 498 GLN cc_start: 0.7862 (mt0) cc_final: 0.7634 (mt0) REVERT: A 572 MET cc_start: 0.6549 (mtt) cc_final: 0.6277 (mtt) REVERT: A 600 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 627 TYR cc_start: 0.6952 (m-80) cc_final: 0.6725 (m-80) REVERT: B 496 PHE cc_start: 0.6833 (t80) cc_final: 0.6627 (m-80) REVERT: B 498 GLN cc_start: 0.7794 (mt0) cc_final: 0.7563 (mt0) REVERT: B 600 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 671 TYR cc_start: 0.8446 (t80) cc_final: 0.8223 (t80) REVERT: C 496 PHE cc_start: 0.6931 (t80) cc_final: 0.6620 (m-80) REVERT: C 498 GLN cc_start: 0.7756 (mt0) cc_final: 0.7523 (mt0) REVERT: C 671 TYR cc_start: 0.8433 (t80) cc_final: 0.8211 (t80) REVERT: D 496 PHE cc_start: 0.7087 (t80) cc_final: 0.6830 (m-80) REVERT: D 498 GLN cc_start: 0.7739 (mt0) cc_final: 0.7497 (mt0) REVERT: D 572 MET cc_start: 0.6488 (mtt) cc_final: 0.6222 (mtt) REVERT: D 600 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7169 (mm-30) REVERT: D 627 TYR cc_start: 0.6882 (m-80) cc_final: 0.6651 (m-80) REVERT: D 671 TYR cc_start: 0.8378 (t80) cc_final: 0.8123 (t80) REVERT: D 677 MET cc_start: 0.7261 (tpp) cc_final: 0.6773 (tpp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1076 time to fit residues: 69.3167 Evaluate side-chains 289 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN B 408 ASN C 408 ASN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.184520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120219 restraints weight = 21005.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124981 restraints weight = 9933.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127900 restraints weight = 6716.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129367 restraints weight = 5415.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130489 restraints weight = 4850.626| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15904 Z= 0.152 Angle : 0.617 10.357 21564 Z= 0.316 Chirality : 0.040 0.182 2476 Planarity : 0.004 0.064 2620 Dihedral : 23.624 175.635 2616 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.85 % Allowed : 11.90 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1956 helix: 1.04 (0.14), residues: 1276 sheet: -3.01 (0.40), residues: 108 loop : -0.46 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 420 TYR 0.011 0.001 TYR A 441 PHE 0.033 0.002 PHE C 742 TRP 0.024 0.002 TRP C 740 HIS 0.011 0.002 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00331 (15900) covalent geometry : angle 0.61700 (21556) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.56512 ( 8) hydrogen bonds : bond 0.04505 ( 1013) hydrogen bonds : angle 4.89192 ( 2943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 321 time to evaluate : 0.550 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 289 HIS cc_start: 0.9107 (m90) cc_final: 0.8666 (m90) REVERT: A 435 TYR cc_start: 0.8602 (m-80) cc_final: 0.8389 (m-80) REVERT: A 494 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 498 GLN cc_start: 0.8231 (mt0) cc_final: 0.7732 (mt0) REVERT: A 739 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7640 (mtm-85) REVERT: B 435 TYR cc_start: 0.8633 (m-80) cc_final: 0.8396 (m-80) REVERT: B 494 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 496 PHE cc_start: 0.7593 (t80) cc_final: 0.6915 (m-10) REVERT: B 498 GLN cc_start: 0.8142 (mt0) cc_final: 0.7730 (mt0) REVERT: B 660 ILE cc_start: 0.9003 (tp) cc_final: 0.8793 (tp) REVERT: B 671 TYR cc_start: 0.8591 (t80) cc_final: 0.8227 (t80) REVERT: C 293 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8158 (mt-10) REVERT: C 494 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7538 (tm-30) REVERT: C 496 PHE cc_start: 0.7672 (t80) cc_final: 0.6903 (m-10) REVERT: C 498 GLN cc_start: 0.8150 (mt0) cc_final: 0.7718 (mt0) REVERT: C 572 MET cc_start: 0.7467 (mtt) cc_final: 0.7233 (mtt) REVERT: C 691 GLN cc_start: 0.7545 (pm20) cc_final: 0.7255 (pm20) REVERT: C 739 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.6990 (mtm-85) REVERT: D 289 HIS cc_start: 0.9017 (m90) cc_final: 0.8666 (m90) REVERT: D 494 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7833 (tm-30) REVERT: D 498 GLN cc_start: 0.8216 (mt0) cc_final: 0.7894 (mt0) REVERT: D 654 ASP cc_start: 0.8367 (p0) cc_final: 0.8032 (p0) REVERT: D 671 TYR cc_start: 0.8543 (t80) cc_final: 0.8131 (t80) REVERT: D 677 MET cc_start: 0.7867 (tpp) cc_final: 0.7094 (tpp) outliers start: 12 outliers final: 9 residues processed: 329 average time/residue: 0.1074 time to fit residues: 54.2712 Evaluate side-chains 278 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 424 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 146 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.185179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123651 restraints weight = 21447.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127545 restraints weight = 10546.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129644 restraints weight = 6794.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130496 restraints weight = 5880.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130410 restraints weight = 5278.660| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15904 Z= 0.140 Angle : 0.553 9.654 21564 Z= 0.286 Chirality : 0.038 0.169 2476 Planarity : 0.003 0.035 2620 Dihedral : 22.243 175.895 2616 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.97 % Allowed : 15.07 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1956 helix: 1.44 (0.14), residues: 1280 sheet: -3.49 (0.52), residues: 56 loop : -0.42 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 420 TYR 0.010 0.001 TYR C 435 PHE 0.026 0.001 PHE C 742 TRP 0.018 0.002 TRP B 740 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00315 (15900) covalent geometry : angle 0.55326 (21556) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.44198 ( 8) hydrogen bonds : bond 0.03951 ( 1013) hydrogen bonds : angle 4.55627 ( 2943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 0.364 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 289 HIS cc_start: 0.9269 (m90) cc_final: 0.8697 (m90) REVERT: A 435 TYR cc_start: 0.8650 (m-80) cc_final: 0.8371 (m-80) REVERT: A 498 GLN cc_start: 0.8147 (mt0) cc_final: 0.7536 (mt0) REVERT: A 691 GLN cc_start: 0.7489 (pm20) cc_final: 0.6855 (mp10) REVERT: A 725 LEU cc_start: 0.7863 (tp) cc_final: 0.7658 (mt) REVERT: A 740 TRP cc_start: 0.7908 (m100) cc_final: 0.7372 (m100) REVERT: B 289 HIS cc_start: 0.9140 (m90) cc_final: 0.8759 (m90) REVERT: B 412 MET cc_start: 0.8830 (mtm) cc_final: 0.8628 (mtt) REVERT: B 420 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7346 (ptp-110) REVERT: B 435 TYR cc_start: 0.8630 (m-80) cc_final: 0.8341 (m-80) REVERT: B 494 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 498 GLN cc_start: 0.8125 (mt0) cc_final: 0.7785 (mt0) REVERT: B 739 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7625 (mtm-85) REVERT: B 740 TRP cc_start: 0.8025 (m100) cc_final: 0.7691 (m100) REVERT: C 494 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 498 GLN cc_start: 0.8157 (mt0) cc_final: 0.7815 (mt0) REVERT: C 653 TYR cc_start: 0.8670 (p90) cc_final: 0.8418 (p90) REVERT: C 691 GLN cc_start: 0.7626 (pm20) cc_final: 0.7322 (pm20) REVERT: C 739 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7189 (mtm-85) REVERT: C 740 TRP cc_start: 0.7930 (m100) cc_final: 0.7576 (m100) REVERT: D 289 HIS cc_start: 0.9141 (m90) cc_final: 0.8640 (m90) REVERT: D 494 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 498 GLN cc_start: 0.8188 (mt0) cc_final: 0.7755 (mt0) REVERT: D 691 GLN cc_start: 0.7512 (pm20) cc_final: 0.6932 (mp10) REVERT: D 739 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7685 (mtm-85) outliers start: 28 outliers final: 17 residues processed: 300 average time/residue: 0.1015 time to fit residues: 47.1393 Evaluate side-chains 286 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 159 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 150 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN B 700 GLN C 700 GLN D 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119258 restraints weight = 21491.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124328 restraints weight = 9782.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127443 restraints weight = 6427.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129023 restraints weight = 5102.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130018 restraints weight = 4510.056| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15904 Z= 0.117 Angle : 0.523 7.466 21564 Z= 0.270 Chirality : 0.038 0.166 2476 Planarity : 0.003 0.035 2620 Dihedral : 21.190 179.306 2616 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 16.34 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1956 helix: 1.71 (0.14), residues: 1280 sheet: -3.36 (0.51), residues: 56 loop : -0.36 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 420 TYR 0.010 0.001 TYR D 309 PHE 0.021 0.001 PHE C 742 TRP 0.018 0.002 TRP C 372 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00252 (15900) covalent geometry : angle 0.52330 (21556) SS BOND : bond 0.00024 ( 4) SS BOND : angle 0.29188 ( 8) hydrogen bonds : bond 0.03700 ( 1013) hydrogen bonds : angle 4.31375 ( 2943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.622 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: A 289 HIS cc_start: 0.9189 (m90) cc_final: 0.8632 (m90) REVERT: A 435 TYR cc_start: 0.8621 (m-80) cc_final: 0.8333 (m-80) REVERT: A 494 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 498 GLN cc_start: 0.7905 (mt0) cc_final: 0.7369 (mt0) REVERT: A 646 ASP cc_start: 0.8427 (p0) cc_final: 0.7939 (p0) REVERT: A 691 GLN cc_start: 0.7444 (pm20) cc_final: 0.6830 (mp10) REVERT: B 289 HIS cc_start: 0.9171 (m90) cc_final: 0.8702 (m90) REVERT: B 420 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7320 (ttm110) REVERT: B 435 TYR cc_start: 0.8599 (m-80) cc_final: 0.8288 (m-80) REVERT: B 494 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 498 GLN cc_start: 0.8115 (mt0) cc_final: 0.7447 (mt0) REVERT: B 562 MET cc_start: 0.8124 (mpp) cc_final: 0.7878 (mtm) REVERT: B 568 MET cc_start: 0.8149 (mtm) cc_final: 0.7565 (mtm) REVERT: B 646 ASP cc_start: 0.8458 (p0) cc_final: 0.7952 (p0) REVERT: B 691 GLN cc_start: 0.7551 (pm20) cc_final: 0.6910 (mp10) REVERT: B 739 ARG cc_start: 0.7984 (mtm180) cc_final: 0.6948 (mtt90) REVERT: B 742 PHE cc_start: 0.7688 (t80) cc_final: 0.7273 (t80) REVERT: C 339 LEU cc_start: 0.8809 (mt) cc_final: 0.8471 (mt) REVERT: C 494 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 498 GLN cc_start: 0.8081 (mt0) cc_final: 0.7408 (mt0) REVERT: C 547 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8185 (ttp) REVERT: C 568 MET cc_start: 0.8166 (mtm) cc_final: 0.7520 (mtm) REVERT: C 691 GLN cc_start: 0.7585 (pm20) cc_final: 0.6979 (mp10) REVERT: C 710 LYS cc_start: 0.7903 (ptpt) cc_final: 0.7673 (pttt) REVERT: C 739 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: D 289 HIS cc_start: 0.9083 (m90) cc_final: 0.8632 (m90) REVERT: D 494 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7846 (tm-30) REVERT: D 498 GLN cc_start: 0.8186 (mt0) cc_final: 0.7938 (mt0) REVERT: D 568 MET cc_start: 0.8235 (mtm) cc_final: 0.7995 (mtm) REVERT: D 646 ASP cc_start: 0.8465 (p0) cc_final: 0.7970 (p0) REVERT: D 691 GLN cc_start: 0.7511 (pm20) cc_final: 0.6928 (mp10) outliers start: 33 outliers final: 26 residues processed: 316 average time/residue: 0.1171 time to fit residues: 57.2186 Evaluate side-chains 296 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 687 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 86 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118551 restraints weight = 21463.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123544 restraints weight = 9897.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126672 restraints weight = 6551.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128464 restraints weight = 5201.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129365 restraints weight = 4581.113| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15904 Z= 0.120 Angle : 0.521 10.162 21564 Z= 0.267 Chirality : 0.038 0.156 2476 Planarity : 0.003 0.042 2620 Dihedral : 20.226 179.322 2616 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.11 % Allowed : 18.87 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 1956 helix: 1.76 (0.15), residues: 1288 sheet: -3.43 (0.49), residues: 56 loop : -0.33 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 420 TYR 0.010 0.001 TYR C 435 PHE 0.029 0.001 PHE C 742 TRP 0.029 0.002 TRP D 749 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00266 (15900) covalent geometry : angle 0.52127 (21556) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.29619 ( 8) hydrogen bonds : bond 0.03595 ( 1013) hydrogen bonds : angle 4.15647 ( 2943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 0.718 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: A 289 HIS cc_start: 0.9182 (m90) cc_final: 0.8632 (m90) REVERT: A 420 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7348 (ptp-110) REVERT: A 435 TYR cc_start: 0.8579 (m-80) cc_final: 0.8222 (m-80) REVERT: A 498 GLN cc_start: 0.8009 (mt0) cc_final: 0.7735 (mt0) REVERT: A 568 MET cc_start: 0.8278 (mtm) cc_final: 0.7487 (mtm) REVERT: A 646 ASP cc_start: 0.8421 (p0) cc_final: 0.7946 (p0) REVERT: A 691 GLN cc_start: 0.7475 (pm20) cc_final: 0.6876 (mp10) REVERT: B 289 HIS cc_start: 0.9161 (m90) cc_final: 0.8631 (m90) REVERT: B 419 ASN cc_start: 0.7978 (t0) cc_final: 0.7623 (m-40) REVERT: B 420 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7113 (ttm110) REVERT: B 435 TYR cc_start: 0.8578 (m-80) cc_final: 0.8224 (m-80) REVERT: B 498 GLN cc_start: 0.8125 (mt0) cc_final: 0.7742 (mt0) REVERT: B 562 MET cc_start: 0.8189 (mpp) cc_final: 0.7838 (mtm) REVERT: B 646 ASP cc_start: 0.8496 (p0) cc_final: 0.7977 (p0) REVERT: B 691 GLN cc_start: 0.7537 (pm20) cc_final: 0.6911 (mp10) REVERT: B 739 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7781 (mtm180) REVERT: B 742 PHE cc_start: 0.7670 (t80) cc_final: 0.7254 (t80) REVERT: C 339 LEU cc_start: 0.8801 (mt) cc_final: 0.8479 (mt) REVERT: C 420 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7353 (ptp-110) REVERT: C 498 GLN cc_start: 0.8081 (mt0) cc_final: 0.7558 (mt0) REVERT: C 547 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8096 (ttp) REVERT: C 691 GLN cc_start: 0.7594 (pm20) cc_final: 0.6980 (mp10) REVERT: C 739 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: C 742 PHE cc_start: 0.7980 (t80) cc_final: 0.7571 (t80) REVERT: D 289 HIS cc_start: 0.9107 (m90) cc_final: 0.8626 (m90) REVERT: D 547 MET cc_start: 0.8498 (ttm) cc_final: 0.8121 (ttp) REVERT: D 646 ASP cc_start: 0.8497 (p0) cc_final: 0.7985 (p0) REVERT: D 677 MET cc_start: 0.7727 (tpp) cc_final: 0.7476 (tpp) REVERT: D 691 GLN cc_start: 0.7594 (pm20) cc_final: 0.7004 (mp10) REVERT: D 742 PHE cc_start: 0.7703 (t80) cc_final: 0.7345 (t80) outliers start: 30 outliers final: 22 residues processed: 295 average time/residue: 0.1237 time to fit residues: 56.2815 Evaluate side-chains 281 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 71 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118330 restraints weight = 21424.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123347 restraints weight = 9998.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126470 restraints weight = 6616.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128225 restraints weight = 5266.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129334 restraints weight = 4628.872| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15904 Z= 0.117 Angle : 0.534 11.071 21564 Z= 0.268 Chirality : 0.038 0.162 2476 Planarity : 0.003 0.041 2620 Dihedral : 18.760 174.385 2616 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.39 % Allowed : 19.23 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1956 helix: 1.85 (0.15), residues: 1288 sheet: -3.37 (0.48), residues: 56 loop : -0.29 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 420 TYR 0.009 0.001 TYR C 435 PHE 0.027 0.001 PHE C 742 TRP 0.020 0.002 TRP C 372 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00259 (15900) covalent geometry : angle 0.53391 (21556) SS BOND : bond 0.00008 ( 4) SS BOND : angle 0.38108 ( 8) hydrogen bonds : bond 0.03509 ( 1013) hydrogen bonds : angle 4.04960 ( 2943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.885 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: A 289 HIS cc_start: 0.9172 (m90) cc_final: 0.8622 (m90) REVERT: A 420 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7308 (ptp-110) REVERT: A 435 TYR cc_start: 0.8556 (m-80) cc_final: 0.8177 (m-80) REVERT: A 498 GLN cc_start: 0.8007 (mt0) cc_final: 0.7546 (mt0) REVERT: A 568 MET cc_start: 0.8348 (mtm) cc_final: 0.7761 (mtm) REVERT: A 646 ASP cc_start: 0.8504 (p0) cc_final: 0.8030 (p0) REVERT: A 691 GLN cc_start: 0.7482 (pm20) cc_final: 0.6907 (mp10) REVERT: B 289 HIS cc_start: 0.9085 (m90) cc_final: 0.8526 (m90) REVERT: B 419 ASN cc_start: 0.7996 (t0) cc_final: 0.7652 (m-40) REVERT: B 420 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7151 (ttm110) REVERT: B 435 TYR cc_start: 0.8548 (m-80) cc_final: 0.8184 (m-80) REVERT: B 498 GLN cc_start: 0.8025 (mt0) cc_final: 0.7569 (mt0) REVERT: B 562 MET cc_start: 0.8187 (mpp) cc_final: 0.7832 (mtm) REVERT: B 568 MET cc_start: 0.8193 (mtm) cc_final: 0.7692 (mtm) REVERT: B 646 ASP cc_start: 0.8543 (p0) cc_final: 0.8052 (p0) REVERT: B 691 GLN cc_start: 0.7541 (pm20) cc_final: 0.6923 (mp10) REVERT: B 742 PHE cc_start: 0.7717 (t80) cc_final: 0.7215 (t80) REVERT: C 339 LEU cc_start: 0.8856 (mt) cc_final: 0.8551 (mt) REVERT: C 419 ASN cc_start: 0.7892 (t0) cc_final: 0.7528 (m-40) REVERT: C 498 GLN cc_start: 0.8078 (mt0) cc_final: 0.7629 (mt0) REVERT: C 547 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8206 (ttp) REVERT: C 691 GLN cc_start: 0.7600 (pm20) cc_final: 0.6996 (mp10) REVERT: C 739 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7337 (mtm-85) REVERT: D 289 HIS cc_start: 0.9033 (m90) cc_final: 0.8595 (m90) REVERT: D 494 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 498 GLN cc_start: 0.8111 (mt0) cc_final: 0.7662 (mt0) REVERT: D 547 MET cc_start: 0.8532 (ttm) cc_final: 0.8212 (ttp) REVERT: D 568 MET cc_start: 0.8128 (mtm) cc_final: 0.7499 (mtm) REVERT: D 646 ASP cc_start: 0.8533 (p0) cc_final: 0.8048 (p0) REVERT: D 691 GLN cc_start: 0.7600 (pm20) cc_final: 0.7022 (mp10) REVERT: D 739 ARG cc_start: 0.7676 (mtm180) cc_final: 0.6841 (mtt90) REVERT: D 742 PHE cc_start: 0.7717 (t80) cc_final: 0.7381 (t80) outliers start: 34 outliers final: 27 residues processed: 296 average time/residue: 0.1232 time to fit residues: 55.6334 Evaluate side-chains 283 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 687 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 49 optimal weight: 40.0000 chunk 101 optimal weight: 40.0000 chunk 189 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.182181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121233 restraints weight = 20817.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125794 restraints weight = 10152.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128684 restraints weight = 6785.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130240 restraints weight = 5394.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131212 restraints weight = 4750.381| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15904 Z= 0.122 Angle : 0.541 9.997 21564 Z= 0.271 Chirality : 0.038 0.179 2476 Planarity : 0.003 0.052 2620 Dihedral : 17.898 173.835 2616 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.25 % Allowed : 19.79 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.20), residues: 1956 helix: 1.92 (0.15), residues: 1288 sheet: -3.22 (0.45), residues: 56 loop : -0.21 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 420 TYR 0.015 0.001 TYR A 511 PHE 0.030 0.001 PHE C 742 TRP 0.020 0.002 TRP D 372 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00273 (15900) covalent geometry : angle 0.54156 (21556) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.30201 ( 8) hydrogen bonds : bond 0.03432 ( 1013) hydrogen bonds : angle 3.96743 ( 2943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.612 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: A 289 HIS cc_start: 0.9150 (m90) cc_final: 0.8620 (m90) REVERT: A 420 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7323 (ptp-110) REVERT: A 435 TYR cc_start: 0.8566 (m-80) cc_final: 0.8205 (m-80) REVERT: A 498 GLN cc_start: 0.8031 (mt0) cc_final: 0.7684 (mt0) REVERT: A 568 MET cc_start: 0.8341 (mtm) cc_final: 0.7729 (mtm) REVERT: A 646 ASP cc_start: 0.8493 (p0) cc_final: 0.8032 (p0) REVERT: A 691 GLN cc_start: 0.7465 (pm20) cc_final: 0.6899 (mp10) REVERT: B 289 HIS cc_start: 0.9029 (m90) cc_final: 0.8498 (m90) REVERT: B 419 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (m-40) REVERT: B 420 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7525 (ttm110) REVERT: B 435 TYR cc_start: 0.8521 (m-80) cc_final: 0.8159 (m-80) REVERT: B 498 GLN cc_start: 0.8050 (mt0) cc_final: 0.7624 (mt0) REVERT: B 568 MET cc_start: 0.8209 (mtm) cc_final: 0.7554 (mtm) REVERT: B 646 ASP cc_start: 0.8542 (p0) cc_final: 0.8049 (p0) REVERT: B 691 GLN cc_start: 0.7529 (pm20) cc_final: 0.6924 (mp10) REVERT: B 742 PHE cc_start: 0.7830 (t80) cc_final: 0.7561 (t80) REVERT: B 745 ASP cc_start: 0.7977 (m-30) cc_final: 0.6541 (t0) REVERT: C 339 LEU cc_start: 0.8839 (mt) cc_final: 0.8533 (mt) REVERT: C 419 ASN cc_start: 0.7852 (t0) cc_final: 0.7518 (m-40) REVERT: C 420 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7272 (ptp-110) REVERT: C 498 GLN cc_start: 0.8012 (mt0) cc_final: 0.7549 (mt0) REVERT: C 547 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: C 691 GLN cc_start: 0.7591 (pm20) cc_final: 0.6989 (mp10) REVERT: C 739 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7336 (mtm-85) REVERT: D 289 HIS cc_start: 0.9044 (m90) cc_final: 0.8527 (m90) REVERT: D 494 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7586 (tm-30) REVERT: D 498 GLN cc_start: 0.8086 (mt0) cc_final: 0.7508 (mt0) REVERT: D 547 MET cc_start: 0.8471 (ttm) cc_final: 0.8199 (ttp) REVERT: D 568 MET cc_start: 0.8166 (mtm) cc_final: 0.7638 (mtm) REVERT: D 646 ASP cc_start: 0.8538 (p0) cc_final: 0.8061 (p0) REVERT: D 691 GLN cc_start: 0.7583 (pm20) cc_final: 0.7012 (mp10) outliers start: 32 outliers final: 25 residues processed: 289 average time/residue: 0.1215 time to fit residues: 54.1242 Evaluate side-chains 282 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 687 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 174 optimal weight: 0.0070 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122249 restraints weight = 21087.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126840 restraints weight = 10149.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129762 restraints weight = 6745.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131540 restraints weight = 5345.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132359 restraints weight = 4676.973| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15904 Z= 0.111 Angle : 0.556 18.419 21564 Z= 0.273 Chirality : 0.038 0.201 2476 Planarity : 0.003 0.053 2620 Dihedral : 17.330 173.797 2616 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 20.85 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.20), residues: 1956 helix: 1.98 (0.15), residues: 1292 sheet: -3.01 (0.45), residues: 56 loop : -0.14 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 420 TYR 0.014 0.001 TYR A 511 PHE 0.029 0.001 PHE C 742 TRP 0.022 0.002 TRP D 372 HIS 0.003 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00242 (15900) covalent geometry : angle 0.55653 (21556) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.29144 ( 8) hydrogen bonds : bond 0.03384 ( 1013) hydrogen bonds : angle 3.88411 ( 2943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.617 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: A 289 HIS cc_start: 0.9120 (m90) cc_final: 0.8583 (m90) REVERT: A 419 ASN cc_start: 0.8027 (t0) cc_final: 0.7723 (m-40) REVERT: A 420 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7172 (ptp-110) REVERT: A 435 TYR cc_start: 0.8456 (m-80) cc_final: 0.8091 (m-80) REVERT: A 498 GLN cc_start: 0.7987 (mt0) cc_final: 0.7646 (mt0) REVERT: A 568 MET cc_start: 0.8326 (mtm) cc_final: 0.7763 (mtm) REVERT: A 646 ASP cc_start: 0.8492 (p0) cc_final: 0.8050 (p0) REVERT: A 691 GLN cc_start: 0.7458 (pm20) cc_final: 0.6867 (mp10) REVERT: B 289 HIS cc_start: 0.9018 (m90) cc_final: 0.8519 (m90) REVERT: B 419 ASN cc_start: 0.8074 (t0) cc_final: 0.7789 (m-40) REVERT: B 420 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7464 (ttm110) REVERT: B 435 TYR cc_start: 0.8464 (m-80) cc_final: 0.8079 (m-80) REVERT: B 498 GLN cc_start: 0.8009 (mt0) cc_final: 0.7649 (mt0) REVERT: B 568 MET cc_start: 0.8186 (mtm) cc_final: 0.7581 (mtm) REVERT: B 646 ASP cc_start: 0.8534 (p0) cc_final: 0.8065 (p0) REVERT: B 691 GLN cc_start: 0.7536 (pm20) cc_final: 0.6936 (mp10) REVERT: B 742 PHE cc_start: 0.7777 (t80) cc_final: 0.7484 (t80) REVERT: B 745 ASP cc_start: 0.8072 (m-30) cc_final: 0.6599 (t0) REVERT: C 419 ASN cc_start: 0.7912 (t0) cc_final: 0.7620 (m-40) REVERT: C 420 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7254 (ptp-110) REVERT: C 498 GLN cc_start: 0.8020 (mt0) cc_final: 0.7612 (mt0) REVERT: C 547 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: C 691 GLN cc_start: 0.7607 (pm20) cc_final: 0.7010 (mp10) REVERT: C 739 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7438 (mpp-170) REVERT: D 289 HIS cc_start: 0.9016 (m90) cc_final: 0.8518 (m90) REVERT: D 420 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7211 (ptp-110) REVERT: D 494 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 498 GLN cc_start: 0.7890 (mt0) cc_final: 0.7343 (mt0) REVERT: D 547 MET cc_start: 0.8433 (ttm) cc_final: 0.8170 (ttp) REVERT: D 568 MET cc_start: 0.8233 (mtm) cc_final: 0.7743 (mtm) REVERT: D 646 ASP cc_start: 0.8512 (p0) cc_final: 0.8053 (p0) REVERT: D 691 GLN cc_start: 0.7589 (pm20) cc_final: 0.7017 (mp10) REVERT: D 739 ARG cc_start: 0.7594 (mtm180) cc_final: 0.6565 (mtt90) outliers start: 28 outliers final: 24 residues processed: 291 average time/residue: 0.1180 time to fit residues: 53.1877 Evaluate side-chains 288 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 687 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121234 restraints weight = 21029.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125789 restraints weight = 10261.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128730 restraints weight = 6860.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130522 restraints weight = 5427.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131431 restraints weight = 4732.056| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15904 Z= 0.121 Angle : 0.578 16.226 21564 Z= 0.281 Chirality : 0.039 0.198 2476 Planarity : 0.003 0.052 2620 Dihedral : 16.895 169.902 2616 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.11 % Allowed : 20.70 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.20), residues: 1956 helix: 1.90 (0.15), residues: 1316 sheet: -2.91 (0.44), residues: 56 loop : -0.36 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 420 TYR 0.012 0.001 TYR A 511 PHE 0.028 0.001 PHE C 742 TRP 0.023 0.002 TRP C 372 HIS 0.002 0.000 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00268 (15900) covalent geometry : angle 0.57813 (21556) SS BOND : bond 0.00018 ( 4) SS BOND : angle 0.28127 ( 8) hydrogen bonds : bond 0.03367 ( 1013) hydrogen bonds : angle 3.85402 ( 2943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.656 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: A 289 HIS cc_start: 0.9118 (m90) cc_final: 0.8586 (m90) REVERT: A 419 ASN cc_start: 0.8038 (t0) cc_final: 0.7735 (m-40) REVERT: A 420 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7175 (ptp-110) REVERT: A 435 TYR cc_start: 0.8444 (m-80) cc_final: 0.8060 (m-80) REVERT: A 498 GLN cc_start: 0.8019 (mt0) cc_final: 0.7698 (mt0) REVERT: A 568 MET cc_start: 0.8359 (mtm) cc_final: 0.7759 (mtm) REVERT: A 572 MET cc_start: 0.7961 (ptp) cc_final: 0.7700 (ptp) REVERT: A 646 ASP cc_start: 0.8490 (p0) cc_final: 0.8059 (p0) REVERT: A 691 GLN cc_start: 0.7462 (pm20) cc_final: 0.6882 (mp10) REVERT: B 289 HIS cc_start: 0.9031 (m90) cc_final: 0.8529 (m90) REVERT: B 419 ASN cc_start: 0.8088 (t0) cc_final: 0.7820 (m-40) REVERT: B 420 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7481 (ttm110) REVERT: B 435 TYR cc_start: 0.8444 (m-80) cc_final: 0.8083 (m-80) REVERT: B 498 GLN cc_start: 0.7968 (mt0) cc_final: 0.7524 (mt0) REVERT: B 568 MET cc_start: 0.8230 (mtm) cc_final: 0.7724 (mtm) REVERT: B 646 ASP cc_start: 0.8528 (p0) cc_final: 0.8064 (p0) REVERT: B 691 GLN cc_start: 0.7542 (pm20) cc_final: 0.6942 (mp10) REVERT: B 745 ASP cc_start: 0.8067 (m-30) cc_final: 0.6571 (t0) REVERT: C 289 HIS cc_start: 0.8855 (m90) cc_final: 0.8449 (m90) REVERT: C 339 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (mt) REVERT: C 419 ASN cc_start: 0.7920 (t0) cc_final: 0.7654 (m-40) REVERT: C 420 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7278 (ptp-110) REVERT: C 498 GLN cc_start: 0.8001 (mt0) cc_final: 0.7542 (mt0) REVERT: C 646 ASP cc_start: 0.8382 (p0) cc_final: 0.7717 (p0) REVERT: C 691 GLN cc_start: 0.7615 (pm20) cc_final: 0.7018 (mp10) REVERT: D 289 HIS cc_start: 0.9056 (m90) cc_final: 0.8562 (m90) REVERT: D 419 ASN cc_start: 0.7930 (t0) cc_final: 0.7625 (m-40) REVERT: D 420 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7180 (ptp-110) REVERT: D 494 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7494 (tm-30) REVERT: D 498 GLN cc_start: 0.7947 (mt0) cc_final: 0.7405 (mt0) REVERT: D 523 MET cc_start: 0.8952 (tpp) cc_final: 0.8713 (tpt) REVERT: D 547 MET cc_start: 0.8399 (ttm) cc_final: 0.8161 (ttp) REVERT: D 646 ASP cc_start: 0.8502 (p0) cc_final: 0.8054 (p0) REVERT: D 691 GLN cc_start: 0.7597 (pm20) cc_final: 0.7014 (mp10) REVERT: D 739 ARG cc_start: 0.7605 (mtm180) cc_final: 0.6579 (mtt90) outliers start: 30 outliers final: 25 residues processed: 293 average time/residue: 0.1220 time to fit residues: 54.9210 Evaluate side-chains 293 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117971 restraints weight = 21453.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122797 restraints weight = 10596.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125751 restraints weight = 7145.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127603 restraints weight = 5723.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128587 restraints weight = 5022.425| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15904 Z= 0.124 Angle : 0.574 16.376 21564 Z= 0.282 Chirality : 0.039 0.200 2476 Planarity : 0.003 0.048 2620 Dihedral : 16.507 168.494 2616 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.83 % Allowed : 21.06 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.20), residues: 1956 helix: 1.92 (0.15), residues: 1316 sheet: -2.65 (0.48), residues: 56 loop : -0.36 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 420 TYR 0.011 0.001 TYR D 441 PHE 0.027 0.001 PHE C 742 TRP 0.024 0.002 TRP C 372 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00280 (15900) covalent geometry : angle 0.57365 (21556) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.28659 ( 8) hydrogen bonds : bond 0.03375 ( 1013) hydrogen bonds : angle 3.81612 ( 2943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.595 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: A 289 HIS cc_start: 0.9158 (m90) cc_final: 0.8617 (m90) REVERT: A 419 ASN cc_start: 0.8020 (t0) cc_final: 0.7720 (m-40) REVERT: A 420 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7177 (ptp-110) REVERT: A 435 TYR cc_start: 0.8432 (m-80) cc_final: 0.8064 (m-80) REVERT: A 568 MET cc_start: 0.8341 (mtm) cc_final: 0.7742 (mtm) REVERT: A 646 ASP cc_start: 0.8492 (p0) cc_final: 0.8058 (p0) REVERT: A 691 GLN cc_start: 0.7506 (pm20) cc_final: 0.6891 (mp10) REVERT: B 289 HIS cc_start: 0.9081 (m90) cc_final: 0.8724 (m90) REVERT: B 419 ASN cc_start: 0.8076 (t0) cc_final: 0.7800 (m-40) REVERT: B 420 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7520 (ttm110) REVERT: B 435 TYR cc_start: 0.8413 (m-80) cc_final: 0.8040 (m-80) REVERT: B 498 GLN cc_start: 0.7918 (mt0) cc_final: 0.7590 (mt0) REVERT: B 568 MET cc_start: 0.8239 (mtm) cc_final: 0.7633 (mtm) REVERT: B 646 ASP cc_start: 0.8509 (p0) cc_final: 0.8058 (p0) REVERT: B 691 GLN cc_start: 0.7556 (pm20) cc_final: 0.6961 (mp10) REVERT: B 745 ASP cc_start: 0.8085 (m-30) cc_final: 0.6563 (t70) REVERT: C 419 ASN cc_start: 0.7901 (t0) cc_final: 0.7641 (m-40) REVERT: C 420 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7298 (ptp-110) REVERT: C 498 GLN cc_start: 0.7936 (mt0) cc_final: 0.7561 (mt0) REVERT: C 547 MET cc_start: 0.8302 (ttm) cc_final: 0.7997 (ttp) REVERT: C 646 ASP cc_start: 0.8408 (p0) cc_final: 0.7757 (p0) REVERT: C 653 TYR cc_start: 0.8690 (p90) cc_final: 0.8456 (p90) REVERT: C 691 GLN cc_start: 0.7642 (pm20) cc_final: 0.7037 (mp10) REVERT: D 289 HIS cc_start: 0.9141 (m90) cc_final: 0.8654 (m90) REVERT: D 419 ASN cc_start: 0.7953 (t0) cc_final: 0.7649 (m-40) REVERT: D 420 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7160 (ptp-110) REVERT: D 494 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7507 (tm-30) REVERT: D 498 GLN cc_start: 0.7879 (mt0) cc_final: 0.7314 (mt0) REVERT: D 547 MET cc_start: 0.8323 (ttm) cc_final: 0.8024 (ttp) REVERT: D 646 ASP cc_start: 0.8493 (p0) cc_final: 0.8039 (p0) REVERT: D 691 GLN cc_start: 0.7613 (pm20) cc_final: 0.7035 (mp10) REVERT: D 692 GLU cc_start: 0.8163 (tt0) cc_final: 0.7713 (tp30) outliers start: 26 outliers final: 23 residues processed: 281 average time/residue: 0.1178 time to fit residues: 50.9329 Evaluate side-chains 286 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 30.0000 chunk 41 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4197 r_free = 0.4197 target = 0.178485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116790 restraints weight = 21096.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121141 restraints weight = 10525.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123661 restraints weight = 7113.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125419 restraints weight = 5725.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126323 restraints weight = 5035.290| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15904 Z= 0.186 Angle : 0.622 15.691 21564 Z= 0.308 Chirality : 0.041 0.191 2476 Planarity : 0.003 0.048 2620 Dihedral : 16.456 172.974 2616 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.76 % Allowed : 21.27 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.20), residues: 1956 helix: 1.88 (0.15), residues: 1316 sheet: -2.51 (0.49), residues: 56 loop : -0.49 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 420 TYR 0.015 0.001 TYR A 671 PHE 0.027 0.001 PHE C 742 TRP 0.023 0.002 TRP C 372 HIS 0.003 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00434 (15900) covalent geometry : angle 0.62239 (21556) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.43627 ( 8) hydrogen bonds : bond 0.03581 ( 1013) hydrogen bonds : angle 3.89716 ( 2943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.12 seconds wall clock time: 52 minutes 9.05 seconds (3129.05 seconds total)