Starting phenix.real_space_refine on Wed Mar 4 20:22:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_23478_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_23478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_23478.map" model { file = "/net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_23478_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpd_23478/03_2026/7lpd_23478_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15564 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 158 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'LBN:plan-3': 2, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 158 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'LBN:plan-3': 2, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 134 Unusual residues: {'4DY': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'LBN:plan-3': 2, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 9 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: 3.81, per 1000 atoms: 0.24 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: 1.30 Conformation dependent library (CDL) restraints added in 731.3 milliseconds 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: 0.43 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: 2.58 Time building geometry restraints manager: 1.74 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- 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 are 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 : 0.508 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: 0.6550 (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: 0.7793 (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: 0.7755 (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: 0.7088 (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: 0.1297 time to fit residues: 83.2848 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 : 0.596 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120221 restraints weight = 21005.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124959 restraints weight = 9937.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127873 restraints weight = 6716.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129358 restraints weight = 5425.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130330 restraints weight = 4854.664| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 are 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 : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.9144 (m90) cc_final: 0.8702 (m90) REVERT: A 435 TYR cc_start: 0.8605 (m-80) cc_final: 0.8390 (m-80) REVERT: A 494 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 498 GLN cc_start: 0.8232 (mt0) cc_final: 0.7731 (mt0) REVERT: A 739 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7649 (mtm-85) REVERT: B 435 TYR cc_start: 0.8636 (m-80) cc_final: 0.8395 (m-80) REVERT: B 494 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 496 PHE cc_start: 0.7595 (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: 0.9001 (tp) cc_final: 0.8791 (tp) REVERT: B 671 TYR cc_start: 0.8593 (t80) cc_final: 0.8229 (t80) REVERT: C 293 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 494 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 496 PHE cc_start: 0.7675 (t80) cc_final: 0.6903 (m-10) REVERT: C 498 GLN cc_start: 0.8153 (mt0) cc_final: 0.7719 (mt0) REVERT: C 572 MET cc_start: 0.7468 (mtt) cc_final: 0.7234 (mtt) REVERT: C 691 GLN cc_start: 0.7553 (pm20) cc_final: 0.7262 (pm20) REVERT: C 739 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: D 289 HIS cc_start: 0.9049 (m90) cc_final: 0.8693 (m90) REVERT: D 494 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 498 GLN cc_start: 0.8218 (mt0) cc_final: 0.7896 (mt0) REVERT: D 654 ASP cc_start: 0.8363 (p0) cc_final: 0.8029 (p0) REVERT: D 671 TYR cc_start: 0.8545 (t80) cc_final: 0.8132 (t80) REVERT: D 677 MET cc_start: 0.7867 (tpp) cc_final: 0.7092 (tpp) outliers start: 12 outliers final: 9 residues processed: 329 average time/residue: 0.1184 time to fit residues: 60.0508 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 : 0.556 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 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: 0.0670 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.185804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121111 restraints weight = 21400.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125873 restraints weight = 10308.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128777 restraints weight = 6990.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130565 restraints weight = 5648.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131375 restraints weight = 4986.568| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- 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 = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2808 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= 0.133 Angle : 0.548 9.065 21564 Z= 0.283 Chirality : 0.038 0.167 2476 Planarity : 0.003 0.035 2620 Dihedral : 22.273 176.109 2616 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.04 % Allowed : 15.00 % 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 are 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 0.008 0.001 ARG B 420 TYR 0.011 0.001 TYR C 435 PHE 0.025 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 0.00295 (15900) covalent geometry : angle 0.54800 (21556) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.43956 ( 8) hydrogen bonds : bond 0.03937 ( 1013) hydrogen bonds : angle 4.54807 ( 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 319 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.466 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: 0.9175 (m90) cc_final: 0.8611 (m90) REVERT: A 435 TYR cc_start: 0.8638 (m-80) cc_final: 0.8363 (m-80) REVERT: A 498 GLN cc_start: 0.8138 (mt0) cc_final: 0.7513 (mt0) REVERT: A 691 GLN cc_start: 0.7405 (pm20) cc_final: 0.6800 (mp10) REVERT: A 740 TRP cc_start: 0.7827 (m100) cc_final: 0.7419 (m100) REVERT: B 420 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7327 (ptp-110) REVERT: B 435 TYR cc_start: 0.8651 (m-80) cc_final: 0.8359 (m-80) REVERT: B 494 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 498 GLN cc_start: 0.8108 (mt0) cc_final: 0.7770 (mt0) REVERT: B 740 TRP cc_start: 0.7935 (m100) cc_final: 0.7725 (m100) REVERT: C 494 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 498 GLN cc_start: 0.8147 (mt0) cc_final: 0.7805 (mt0) REVERT: C 653 TYR cc_start: 0.8655 (p90) cc_final: 0.8399 (p90) REVERT: C 691 GLN cc_start: 0.7561 (pm20) cc_final: 0.7274 (pm20) REVERT: C 739 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7318 (mtm180) REVERT: C 740 TRP cc_start: 0.7858 (m100) cc_final: 0.7628 (m100) REVERT: D 289 HIS cc_start: 0.9034 (m90) cc_final: 0.8540 (m90) REVERT: D 494 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 498 GLN cc_start: 0.8161 (mt0) cc_final: 0.7737 (mt0) REVERT: D 691 GLN cc_start: 0.7466 (pm20) cc_final: 0.6900 (mp10) REVERT: D 739 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7557 (mtm-85) outliers start: 29 outliers final: 18 residues processed: 303 average time/residue: 0.1149 time to fit residues: 54.0567 Evaluate side-chains 285 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 424 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: 6.9990 chunk 22 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 150 optimal weight: 40.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN D 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119290 restraints weight = 21448.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124400 restraints weight = 9755.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127496 restraints weight = 6396.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129172 restraints weight = 5071.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130235 restraints weight = 4471.729| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15904 Z= 0.117 Angle : 0.525 7.429 21564 Z= 0.270 Chirality : 0.039 0.202 2476 Planarity : 0.003 0.036 2620 Dihedral : 21.229 179.180 2616 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.32 % Allowed : 16.48 % Favored : 81.20 % 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 are not related in a simple way. whole: 1.32 (0.19), residues: 1956 helix: 1.69 (0.14), residues: 1280 sheet: -3.35 (0.52), residues: 56 loop : -0.35 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 420 TYR 0.011 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 0.00253 (15900) covalent geometry : angle 0.52505 (21556) SS BOND : bond 0.00022 ( 4) SS BOND : angle 0.28592 ( 8) hydrogen bonds : bond 0.03704 ( 1013) hydrogen bonds : angle 4.31750 ( 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 322 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.497 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: 0.9167 (m90) cc_final: 0.8619 (m90) REVERT: A 435 TYR cc_start: 0.8615 (m-80) cc_final: 0.8332 (m-80) REVERT: A 494 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 498 GLN cc_start: 0.7889 (mt0) cc_final: 0.7389 (mt0) REVERT: A 646 ASP cc_start: 0.8431 (p0) cc_final: 0.7945 (p0) REVERT: A 691 GLN cc_start: 0.7440 (pm20) cc_final: 0.6827 (mp10) REVERT: B 289 HIS cc_start: 0.9141 (m90) cc_final: 0.8705 (m90) REVERT: B 420 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7352 (ttm110) REVERT: B 435 TYR cc_start: 0.8595 (m-80) cc_final: 0.8287 (m-80) REVERT: B 498 GLN cc_start: 0.8095 (mt0) cc_final: 0.7661 (mt0) REVERT: B 562 MET cc_start: 0.8129 (mpp) cc_final: 0.7873 (mtm) REVERT: B 568 MET cc_start: 0.8128 (mtm) cc_final: 0.7587 (mtm) REVERT: B 646 ASP cc_start: 0.8453 (p0) cc_final: 0.7943 (p0) REVERT: B 691 GLN cc_start: 0.7544 (pm20) cc_final: 0.6914 (mp10) REVERT: C 339 LEU cc_start: 0.8821 (mt) cc_final: 0.8476 (mt) REVERT: C 494 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7487 (tm-30) REVERT: C 498 GLN cc_start: 0.8070 (mt0) cc_final: 0.7391 (mt0) REVERT: C 547 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8171 (ttp) REVERT: C 568 MET cc_start: 0.8160 (mtm) cc_final: 0.7523 (mtm) REVERT: C 653 TYR cc_start: 0.8668 (p90) cc_final: 0.8409 (p90) REVERT: C 691 GLN cc_start: 0.7583 (pm20) cc_final: 0.6978 (mp10) REVERT: C 710 LYS cc_start: 0.7887 (ptpt) cc_final: 0.7678 (pttt) REVERT: D 289 HIS cc_start: 0.9058 (m90) cc_final: 0.8617 (m90) REVERT: D 494 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 498 GLN cc_start: 0.8187 (mt0) cc_final: 0.7941 (mt0) REVERT: D 568 MET cc_start: 0.8234 (mtm) cc_final: 0.8002 (mtm) REVERT: D 646 ASP cc_start: 0.8456 (p0) cc_final: 0.7967 (p0) REVERT: D 691 GLN cc_start: 0.7519 (pm20) cc_final: 0.6946 (mp10) outliers start: 33 outliers final: 26 residues processed: 308 average time/residue: 0.1101 time to fit residues: 52.9029 Evaluate side-chains 295 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 5.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 86 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 = 0.183487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119931 restraints weight = 21400.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125103 restraints weight = 9811.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128280 restraints weight = 6440.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130017 restraints weight = 5099.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131098 restraints weight = 4484.506| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15904 Z= 0.112 Angle : 0.519 11.452 21564 Z= 0.264 Chirality : 0.038 0.168 2476 Planarity : 0.003 0.044 2620 Dihedral : 19.942 177.910 2616 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.90 % Allowed : 18.80 % Favored : 79.30 % 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 are not related in a simple way. whole: 1.46 (0.20), residues: 1956 helix: 1.80 (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 0.011 0.001 ARG D 420 TYR 0.010 0.001 TYR C 435 PHE 0.030 0.001 PHE C 742 TRP 0.029 0.002 TRP D 749 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00235 (15900) covalent geometry : angle 0.51948 (21556) SS BOND : bond 0.00046 ( 4) SS BOND : angle 0.30782 ( 8) hydrogen bonds : bond 0.03517 ( 1013) hydrogen bonds : angle 4.08671 ( 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 315 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 0.704 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: 0.9162 (m90) cc_final: 0.8627 (m90) REVERT: A 420 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7310 (ptp-110) REVERT: A 435 TYR cc_start: 0.8560 (m-80) cc_final: 0.8223 (m-80) REVERT: A 476 THR cc_start: 0.8903 (m) cc_final: 0.8685 (t) REVERT: A 498 GLN cc_start: 0.7896 (mt0) cc_final: 0.7620 (mt0) REVERT: A 568 MET cc_start: 0.8411 (mtm) cc_final: 0.7596 (mtm) REVERT: A 646 ASP cc_start: 0.8400 (p0) cc_final: 0.7924 (p0) REVERT: A 691 GLN cc_start: 0.7455 (pm20) cc_final: 0.6870 (mp10) REVERT: A 739 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7631 (mtm-85) REVERT: B 289 HIS cc_start: 0.9090 (m90) cc_final: 0.8690 (m90) REVERT: B 419 ASN cc_start: 0.7978 (t0) cc_final: 0.7644 (m-40) REVERT: B 420 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7123 (ttm110) REVERT: B 435 TYR cc_start: 0.8555 (m-80) cc_final: 0.8193 (m-80) REVERT: B 494 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 498 GLN cc_start: 0.8089 (mt0) cc_final: 0.7621 (mt0) REVERT: B 562 MET cc_start: 0.8186 (mpp) cc_final: 0.7827 (mtm) REVERT: B 646 ASP cc_start: 0.8462 (p0) cc_final: 0.7962 (p0) REVERT: B 691 GLN cc_start: 0.7542 (pm20) cc_final: 0.6920 (mp10) REVERT: B 740 TRP cc_start: 0.7872 (m100) cc_final: 0.7278 (m100) REVERT: B 742 PHE cc_start: 0.7632 (t80) cc_final: 0.7269 (t80) REVERT: C 339 LEU cc_start: 0.8813 (mt) cc_final: 0.8497 (mt) REVERT: C 420 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7361 (ptp-110) REVERT: C 494 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 498 GLN cc_start: 0.8070 (mt0) cc_final: 0.7576 (mt0) REVERT: C 547 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (ttp) REVERT: C 562 MET cc_start: 0.8157 (mpp) cc_final: 0.7795 (mtm) REVERT: C 691 GLN cc_start: 0.7587 (pm20) cc_final: 0.6979 (mp10) REVERT: C 742 PHE cc_start: 0.8006 (t80) cc_final: 0.7611 (t80) REVERT: D 289 HIS cc_start: 0.9084 (m90) cc_final: 0.8615 (m90) REVERT: D 547 MET cc_start: 0.8477 (ttm) cc_final: 0.8154 (ttp) REVERT: D 646 ASP cc_start: 0.8473 (p0) cc_final: 0.7964 (p0) REVERT: D 691 GLN cc_start: 0.7597 (pm20) cc_final: 0.7021 (mp10) REVERT: D 739 ARG cc_start: 0.7824 (mtm180) cc_final: 0.6949 (mtt90) REVERT: D 742 PHE cc_start: 0.7728 (t80) cc_final: 0.7374 (t80) outliers start: 27 outliers final: 20 residues processed: 301 average time/residue: 0.1242 time to fit residues: 57.1928 Evaluate side-chains 284 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 514 ILE 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: 0.0570 chunk 74 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.183923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122764 restraints weight = 20897.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127396 restraints weight = 10083.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130302 restraints weight = 6710.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131890 restraints weight = 5316.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133047 restraints weight = 4667.869| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15904 Z= 0.114 Angle : 0.537 18.076 21564 Z= 0.266 Chirality : 0.038 0.171 2476 Planarity : 0.003 0.043 2620 Dihedral : 18.642 177.059 2616 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.32 % Allowed : 18.94 % Favored : 78.73 % 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 are not related in a simple way. whole: 1.58 (0.19), residues: 1956 helix: 1.90 (0.14), residues: 1288 sheet: -3.39 (0.46), residues: 56 loop : -0.28 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 420 TYR 0.010 0.001 TYR B 555 PHE 0.026 0.001 PHE C 742 TRP 0.019 0.002 TRP A 372 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00250 (15900) covalent geometry : angle 0.53688 (21556) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.37375 ( 8) hydrogen bonds : bond 0.03440 ( 1013) hydrogen bonds : angle 4.00011 ( 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 309 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.574 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: 0.9111 (m90) cc_final: 0.8575 (m90) REVERT: A 420 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7279 (ptp-110) REVERT: A 435 TYR cc_start: 0.8550 (m-80) cc_final: 0.8178 (m-80) REVERT: A 476 THR cc_start: 0.8909 (m) cc_final: 0.8700 (t) REVERT: A 498 GLN cc_start: 0.8000 (mt0) cc_final: 0.7536 (mt0) REVERT: A 568 MET cc_start: 0.8335 (mtm) cc_final: 0.7754 (mtm) REVERT: A 646 ASP cc_start: 0.8479 (p0) cc_final: 0.8008 (p0) REVERT: A 691 GLN cc_start: 0.7449 (pm20) cc_final: 0.6887 (mp10) REVERT: A 739 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7408 (mtm-85) REVERT: B 289 HIS cc_start: 0.9012 (m90) cc_final: 0.8611 (m90) REVERT: B 419 ASN cc_start: 0.8014 (t0) cc_final: 0.7700 (m-40) REVERT: B 420 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7180 (ttm110) REVERT: B 435 TYR cc_start: 0.8514 (m-80) cc_final: 0.8175 (m-80) REVERT: B 494 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 498 GLN cc_start: 0.8022 (mt0) cc_final: 0.7493 (mt0) REVERT: B 562 MET cc_start: 0.8169 (mpp) cc_final: 0.7842 (mtm) REVERT: B 568 MET cc_start: 0.8159 (mtm) cc_final: 0.7539 (mtm) REVERT: B 646 ASP cc_start: 0.8522 (p0) cc_final: 0.8030 (p0) REVERT: B 691 GLN cc_start: 0.7524 (pm20) cc_final: 0.6922 (mp10) REVERT: B 742 PHE cc_start: 0.7753 (t80) cc_final: 0.7380 (t80) REVERT: B 745 ASP cc_start: 0.7908 (m-30) cc_final: 0.6529 (t0) REVERT: C 339 LEU cc_start: 0.8868 (mt) cc_final: 0.8565 (mt) REVERT: C 419 ASN cc_start: 0.7923 (t0) cc_final: 0.7584 (m-40) REVERT: C 494 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 498 GLN cc_start: 0.8088 (mt0) cc_final: 0.7708 (mt0) REVERT: C 547 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8198 (ttp) REVERT: C 691 GLN cc_start: 0.7583 (pm20) cc_final: 0.6990 (mp10) REVERT: D 289 HIS cc_start: 0.8955 (m90) cc_final: 0.8478 (m90) REVERT: D 369 PHE cc_start: 0.5731 (m-10) cc_final: 0.5401 (m-10) REVERT: D 494 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 498 GLN cc_start: 0.8078 (mt0) cc_final: 0.7654 (mt0) REVERT: D 547 MET cc_start: 0.8536 (ttm) cc_final: 0.8206 (ttp) REVERT: D 568 MET cc_start: 0.8101 (mtm) cc_final: 0.7458 (mtm) REVERT: D 646 ASP cc_start: 0.8529 (p0) cc_final: 0.8043 (p0) REVERT: D 691 GLN cc_start: 0.7587 (pm20) cc_final: 0.7028 (mp10) REVERT: D 739 ARG cc_start: 0.7756 (mtm180) cc_final: 0.6873 (mtt90) outliers start: 33 outliers final: 26 residues processed: 296 average time/residue: 0.1142 time to fit residues: 52.1607 Evaluate side-chains 286 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 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 654 ASP Chi-restraints excluded: chain D residue 674 LEU 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: 2.9990 chunk 116 optimal weight: 0.7980 chunk 49 optimal weight: 40.0000 chunk 101 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.0370 chunk 175 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.183796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123544 restraints weight = 20727.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128196 restraints weight = 9987.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131070 restraints weight = 6645.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132665 restraints weight = 5261.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133733 restraints weight = 4613.374| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3823 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= 0.107 Angle : 0.534 15.445 21564 Z= 0.266 Chirality : 0.038 0.183 2476 Planarity : 0.003 0.051 2620 Dihedral : 17.565 170.914 2616 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 19.86 % Favored : 78.03 % 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 are not related in a simple way. whole: 1.66 (0.20), residues: 1956 helix: 1.99 (0.15), residues: 1292 sheet: -3.53 (0.34), residues: 96 loop : -0.03 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 420 TYR 0.013 0.001 TYR A 511 PHE 0.031 0.001 PHE C 742 TRP 0.021 0.002 TRP A 372 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00231 (15900) covalent geometry : angle 0.53420 (21556) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.25273 ( 8) hydrogen bonds : bond 0.03352 ( 1013) hydrogen bonds : angle 3.90032 ( 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 308 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 0.523 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: 0.9131 (m90) cc_final: 0.8614 (m90) REVERT: A 419 ASN cc_start: 0.8020 (t0) cc_final: 0.7695 (m-40) REVERT: A 420 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7162 (ptp-110) REVERT: A 435 TYR cc_start: 0.8449 (m-80) cc_final: 0.8080 (m-80) REVERT: A 476 THR cc_start: 0.8909 (m) cc_final: 0.8704 (t) REVERT: A 498 GLN cc_start: 0.8004 (mt0) cc_final: 0.7663 (mt0) REVERT: A 523 MET cc_start: 0.8935 (tpp) cc_final: 0.8704 (tpt) REVERT: A 568 MET cc_start: 0.8344 (mtm) cc_final: 0.7773 (mtm) REVERT: A 646 ASP cc_start: 0.8480 (p0) cc_final: 0.8042 (p0) REVERT: A 691 GLN cc_start: 0.7427 (pm20) cc_final: 0.6856 (mp10) REVERT: A 739 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7335 (mtm-85) REVERT: B 289 HIS cc_start: 0.9011 (m90) cc_final: 0.8668 (m90) REVERT: B 419 ASN cc_start: 0.8056 (t0) cc_final: 0.7774 (m-40) REVERT: B 420 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7513 (ttm110) REVERT: B 435 TYR cc_start: 0.8415 (m-80) cc_final: 0.8052 (m-80) REVERT: B 494 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 498 GLN cc_start: 0.8072 (mt0) cc_final: 0.7452 (mt0) REVERT: B 547 MET cc_start: 0.8451 (ttm) cc_final: 0.8045 (ttp) REVERT: B 568 MET cc_start: 0.8192 (mtm) cc_final: 0.7608 (mtm) REVERT: B 646 ASP cc_start: 0.8519 (p0) cc_final: 0.8052 (p0) REVERT: B 691 GLN cc_start: 0.7524 (pm20) cc_final: 0.6939 (mp10) REVERT: B 742 PHE cc_start: 0.7848 (t80) cc_final: 0.7599 (t80) REVERT: B 745 ASP cc_start: 0.8020 (m-30) cc_final: 0.6620 (t0) REVERT: C 339 LEU cc_start: 0.8826 (mt) cc_final: 0.8534 (mt) REVERT: C 419 ASN cc_start: 0.7793 (t0) cc_final: 0.7471 (m-40) REVERT: C 420 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7238 (ptp-110) REVERT: C 494 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 498 GLN cc_start: 0.8024 (mt0) cc_final: 0.7550 (mt0) REVERT: C 691 GLN cc_start: 0.7583 (pm20) cc_final: 0.6988 (mp10) REVERT: D 289 HIS cc_start: 0.9026 (m90) cc_final: 0.8538 (m90) REVERT: D 369 PHE cc_start: 0.5806 (m-10) cc_final: 0.5492 (m-10) REVERT: D 420 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7173 (ptp-110) REVERT: D 494 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 498 GLN cc_start: 0.8000 (mt0) cc_final: 0.7512 (mt0) REVERT: D 547 MET cc_start: 0.8439 (ttm) cc_final: 0.8141 (ttp) REVERT: D 568 MET cc_start: 0.8153 (mtm) cc_final: 0.7636 (mtm) REVERT: D 646 ASP cc_start: 0.8515 (p0) cc_final: 0.8047 (p0) REVERT: D 691 GLN cc_start: 0.7591 (pm20) cc_final: 0.7041 (mp10) REVERT: D 739 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6977 (mtt90) outliers start: 30 outliers final: 23 residues processed: 297 average time/residue: 0.1152 time to fit residues: 53.0255 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 : 0.660 ------------------------------------------------------------------------------- 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 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 654 ASP Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 395 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 174 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.183136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121505 restraints weight = 21150.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126173 restraints weight = 10190.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129076 restraints weight = 6785.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130638 restraints weight = 5383.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131684 restraints weight = 4742.703| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 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 = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15904 Z= 0.112 Angle : 0.537 15.964 21564 Z= 0.267 Chirality : 0.038 0.178 2476 Planarity : 0.003 0.043 2620 Dihedral : 17.050 170.174 2616 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.83 % Allowed : 20.85 % Favored : 77.32 % 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 are not related in a simple way. whole: 1.68 (0.20), residues: 1956 helix: 2.01 (0.15), residues: 1292 sheet: -3.51 (0.34), residues: 96 loop : -0.02 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 420 TYR 0.011 0.001 TYR A 511 PHE 0.029 0.001 PHE C 742 TRP 0.023 0.002 TRP D 372 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00247 (15900) covalent geometry : angle 0.53730 (21556) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.28456 ( 8) hydrogen bonds : bond 0.03332 ( 1013) hydrogen bonds : angle 3.82528 ( 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 299 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.591 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: 0.9145 (m90) cc_final: 0.8612 (m90) REVERT: A 419 ASN cc_start: 0.8012 (t0) cc_final: 0.7704 (m-40) REVERT: A 420 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7157 (ptp-110) REVERT: A 435 TYR cc_start: 0.8451 (m-80) cc_final: 0.8046 (m-80) REVERT: A 476 THR cc_start: 0.8919 (m) cc_final: 0.8706 (t) REVERT: A 498 GLN cc_start: 0.8015 (mt0) cc_final: 0.7667 (mt0) REVERT: A 523 MET cc_start: 0.8953 (tpp) cc_final: 0.8694 (tpt) REVERT: A 568 MET cc_start: 0.8372 (mtm) cc_final: 0.7774 (mtm) REVERT: A 646 ASP cc_start: 0.8497 (p0) cc_final: 0.8036 (p0) REVERT: A 691 GLN cc_start: 0.7464 (pm20) cc_final: 0.6880 (mp10) REVERT: B 289 HIS cc_start: 0.9031 (m90) cc_final: 0.8705 (m90) REVERT: B 419 ASN cc_start: 0.8059 (t0) cc_final: 0.7802 (m-40) REVERT: B 420 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7478 (ttm110) REVERT: B 435 TYR cc_start: 0.8418 (m-80) cc_final: 0.8053 (m-80) REVERT: B 494 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 498 GLN cc_start: 0.8065 (mt0) cc_final: 0.7418 (mt0) REVERT: B 547 MET cc_start: 0.8429 (ttm) cc_final: 0.8039 (ttp) REVERT: B 568 MET cc_start: 0.8182 (mtm) cc_final: 0.7588 (mtm) REVERT: B 646 ASP cc_start: 0.8519 (p0) cc_final: 0.8055 (p0) REVERT: B 691 GLN cc_start: 0.7548 (pm20) cc_final: 0.6955 (mp10) REVERT: B 742 PHE cc_start: 0.7728 (t80) cc_final: 0.7421 (t80) REVERT: B 745 ASP cc_start: 0.7970 (m-30) cc_final: 0.6638 (t0) REVERT: C 419 ASN cc_start: 0.7897 (t0) cc_final: 0.7615 (m-40) REVERT: C 420 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7272 (ptp-110) REVERT: C 494 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 498 GLN cc_start: 0.8009 (mt0) cc_final: 0.7536 (mt0) REVERT: C 691 GLN cc_start: 0.7620 (pm20) cc_final: 0.7017 (mp10) REVERT: D 289 HIS cc_start: 0.9080 (m90) cc_final: 0.8614 (m90) REVERT: D 369 PHE cc_start: 0.5896 (m-10) cc_final: 0.5614 (m-10) REVERT: D 419 ASN cc_start: 0.7904 (t0) cc_final: 0.7560 (m-40) REVERT: D 494 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 498 GLN cc_start: 0.8049 (mt0) cc_final: 0.7505 (mt0) REVERT: D 547 MET cc_start: 0.8431 (ttm) cc_final: 0.8168 (ttp) REVERT: D 568 MET cc_start: 0.8218 (mtm) cc_final: 0.7754 (mtm) REVERT: D 646 ASP cc_start: 0.8500 (p0) cc_final: 0.8043 (p0) REVERT: D 691 GLN cc_start: 0.7600 (pm20) cc_final: 0.7019 (mp10) REVERT: D 739 ARG cc_start: 0.7751 (mtm180) cc_final: 0.6879 (mtt90) outliers start: 26 outliers final: 22 residues processed: 289 average time/residue: 0.1144 time to fit residues: 51.7334 Evaluate side-chains 283 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 700 GLN 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 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 524 LEU Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121535 restraints weight = 20995.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126108 restraints weight = 10204.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128987 restraints weight = 6817.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130706 restraints weight = 5413.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131553 restraints weight = 4731.991| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- 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 = 0.91 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 = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4005 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= 0.121 Angle : 0.565 15.332 21564 Z= 0.276 Chirality : 0.039 0.187 2476 Planarity : 0.003 0.059 2620 Dihedral : 16.767 168.612 2616 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.90 % Allowed : 20.99 % 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 are not related in a simple way. whole: 1.72 (0.20), residues: 1956 helix: 2.02 (0.15), residues: 1292 sheet: -3.45 (0.34), residues: 96 loop : 0.03 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 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 A 364 Details of bonding type rmsd covalent geometry : bond 0.00272 (15900) covalent geometry : angle 0.56484 (21556) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.26798 ( 8) hydrogen bonds : bond 0.03371 ( 1013) hydrogen bonds : angle 3.81607 ( 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 302 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 0.573 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: 0.9102 (m90) cc_final: 0.8571 (m90) REVERT: A 419 ASN cc_start: 0.8063 (t0) cc_final: 0.7748 (m-40) REVERT: A 420 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7179 (ptp-110) REVERT: A 435 TYR cc_start: 0.8427 (m-80) cc_final: 0.8063 (m-80) REVERT: A 476 THR cc_start: 0.8924 (m) cc_final: 0.8702 (t) REVERT: A 498 GLN cc_start: 0.8050 (mt0) cc_final: 0.7756 (mt0) REVERT: A 523 MET cc_start: 0.8958 (tpp) cc_final: 0.8755 (tpt) REVERT: A 547 MET cc_start: 0.8445 (ttp) cc_final: 0.8061 (ttp) REVERT: A 568 MET cc_start: 0.8357 (mtm) cc_final: 0.7756 (mtm) REVERT: A 646 ASP cc_start: 0.8511 (p0) cc_final: 0.8056 (p0) REVERT: A 691 GLN cc_start: 0.7458 (pm20) cc_final: 0.6877 (mp10) REVERT: B 289 HIS cc_start: 0.8979 (m90) cc_final: 0.8674 (m90) REVERT: B 419 ASN cc_start: 0.8076 (t0) cc_final: 0.7834 (m-40) REVERT: B 420 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7492 (ttm110) REVERT: B 435 TYR cc_start: 0.8402 (m-80) cc_final: 0.8029 (m-80) REVERT: B 494 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 498 GLN cc_start: 0.8030 (mt0) cc_final: 0.7510 (mt0) REVERT: B 547 MET cc_start: 0.8432 (ttm) cc_final: 0.8047 (ttp) REVERT: B 568 MET cc_start: 0.8232 (mtm) cc_final: 0.7721 (mtm) REVERT: B 646 ASP cc_start: 0.8520 (p0) cc_final: 0.8063 (p0) REVERT: B 691 GLN cc_start: 0.7552 (pm20) cc_final: 0.6957 (mp10) REVERT: B 745 ASP cc_start: 0.7944 (m-30) cc_final: 0.6632 (t0) REVERT: C 339 LEU cc_start: 0.8698 (mt) cc_final: 0.8409 (mt) REVERT: C 419 ASN cc_start: 0.7921 (t0) cc_final: 0.7667 (m-40) REVERT: C 420 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7287 (ptp-110) REVERT: C 494 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 498 GLN cc_start: 0.8024 (mt0) cc_final: 0.7539 (mt0) REVERT: C 547 MET cc_start: 0.8260 (ttm) cc_final: 0.8047 (ttp) REVERT: C 572 MET cc_start: 0.8048 (ptp) cc_final: 0.7847 (ptp) REVERT: C 646 ASP cc_start: 0.8384 (p0) cc_final: 0.7711 (p0) REVERT: C 691 GLN cc_start: 0.7609 (pm20) cc_final: 0.7014 (mp10) REVERT: C 739 ARG cc_start: 0.7337 (mpt90) cc_final: 0.6620 (mpt-90) REVERT: D 289 HIS cc_start: 0.9050 (m90) cc_final: 0.8585 (m90) REVERT: D 419 ASN cc_start: 0.7939 (t0) cc_final: 0.7650 (m-40) REVERT: D 420 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7436 (mtp85) REVERT: D 494 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 498 GLN cc_start: 0.8032 (mt0) cc_final: 0.7476 (mt0) REVERT: D 523 MET cc_start: 0.8911 (tpp) cc_final: 0.8664 (tpt) REVERT: D 547 MET cc_start: 0.8413 (ttm) cc_final: 0.8143 (ttp) REVERT: D 646 ASP cc_start: 0.8512 (p0) cc_final: 0.8052 (p0) REVERT: D 691 GLN cc_start: 0.7589 (pm20) cc_final: 0.7021 (mp10) REVERT: D 739 ARG cc_start: 0.7739 (mtm180) cc_final: 0.6869 (mtt90) outliers start: 27 outliers final: 23 residues processed: 291 average time/residue: 0.1175 time to fit residues: 52.9095 Evaluate side-chains 291 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 457 VAL Chi-restraints excluded: chain B residue 465 LEU 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 B residue 700 GLN 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 C residue 692 GLU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.180491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118801 restraints weight = 21064.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123224 restraints weight = 10345.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126083 restraints weight = 6950.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127753 restraints weight = 5534.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128637 restraints weight = 4861.088| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15904 Z= 0.159 Angle : 0.592 14.939 21564 Z= 0.293 Chirality : 0.040 0.199 2476 Planarity : 0.003 0.057 2620 Dihedral : 16.607 171.576 2616 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.69 % Allowed : 21.69 % Favored : 76.62 % 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 are not related in a simple way. whole: 1.57 (0.20), residues: 1956 helix: 1.93 (0.15), residues: 1316 sheet: -3.44 (0.34), residues: 96 loop : -0.23 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 420 TYR 0.013 0.001 TYR A 511 PHE 0.027 0.001 PHE C 742 TRP 0.023 0.002 TRP C 372 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00370 (15900) covalent geometry : angle 0.59199 (21556) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.32877 ( 8) hydrogen bonds : bond 0.03459 ( 1013) hydrogen bonds : angle 3.85588 ( 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: 24 poor density : 269 time to evaluate : 0.555 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: 0.9097 (m90) cc_final: 0.8560 (m90) REVERT: A 419 ASN cc_start: 0.8090 (t0) cc_final: 0.7781 (m-40) REVERT: A 420 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7209 (ptp-110) REVERT: A 435 TYR cc_start: 0.8444 (m-80) cc_final: 0.8067 (m-80) REVERT: A 568 MET cc_start: 0.8404 (mtm) cc_final: 0.7737 (mtm) REVERT: A 646 ASP cc_start: 0.8540 (p0) cc_final: 0.8090 (p0) REVERT: A 691 GLN cc_start: 0.7486 (pm20) cc_final: 0.6892 (mp10) REVERT: B 289 HIS cc_start: 0.8998 (m90) cc_final: 0.8676 (m90) REVERT: B 419 ASN cc_start: 0.8107 (t0) cc_final: 0.7858 (m-40) REVERT: B 420 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7539 (ttm110) REVERT: B 435 TYR cc_start: 0.8418 (m-80) cc_final: 0.8032 (m-80) REVERT: B 498 GLN cc_start: 0.8050 (mt0) cc_final: 0.7674 (mt0) REVERT: B 547 MET cc_start: 0.8457 (ttm) cc_final: 0.8059 (ttp) REVERT: B 568 MET cc_start: 0.8181 (mtm) cc_final: 0.7592 (mtm) REVERT: B 646 ASP cc_start: 0.8556 (p0) cc_final: 0.8104 (p0) REVERT: B 691 GLN cc_start: 0.7569 (pm20) cc_final: 0.6962 (mp10) REVERT: B 745 ASP cc_start: 0.7953 (m-30) cc_final: 0.6607 (t70) REVERT: C 339 LEU cc_start: 0.8624 (mt) cc_final: 0.8264 (mp) REVERT: C 419 ASN cc_start: 0.7902 (t0) cc_final: 0.7631 (m-40) REVERT: C 420 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7231 (ptp90) REVERT: C 494 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 498 GLN cc_start: 0.8001 (mt0) cc_final: 0.7536 (mt0) REVERT: C 646 ASP cc_start: 0.8419 (p0) cc_final: 0.7748 (p0) REVERT: C 691 GLN cc_start: 0.7623 (pm20) cc_final: 0.7028 (mp10) REVERT: C 739 ARG cc_start: 0.7431 (mpt90) cc_final: 0.6724 (mpt-90) REVERT: D 289 HIS cc_start: 0.9078 (m90) cc_final: 0.8616 (m90) REVERT: D 419 ASN cc_start: 0.7972 (t0) cc_final: 0.7682 (m-40) REVERT: D 420 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7452 (mtp85) REVERT: D 494 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 498 GLN cc_start: 0.8092 (mt0) cc_final: 0.7458 (mt0) REVERT: D 547 MET cc_start: 0.8475 (ttm) cc_final: 0.8258 (ttp) REVERT: D 646 ASP cc_start: 0.8555 (p0) cc_final: 0.8095 (p0) REVERT: D 691 GLN cc_start: 0.7596 (pm20) cc_final: 0.7014 (mp10) REVERT: D 739 ARG cc_start: 0.7752 (mtm180) cc_final: 0.6901 (mtt90) outliers start: 24 outliers final: 24 residues processed: 284 average time/residue: 0.1199 time to fit residues: 52.5801 Evaluate side-chains 287 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 457 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain B residue 703 ILE 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 C residue 692 GLU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 465 LEU 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 102 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 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 = 0.4193 r_free = 0.4193 target = 0.178661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117169 restraints weight = 21125.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121497 restraints weight = 10427.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124193 restraints weight = 7016.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125699 restraints weight = 5606.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126774 restraints weight = 4955.153| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15904 Z= 0.198 Angle : 0.614 16.291 21564 Z= 0.309 Chirality : 0.041 0.199 2476 Planarity : 0.003 0.063 2620 Dihedral : 16.586 175.077 2616 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.04 % Allowed : 20.99 % 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 are not related in a simple way. whole: 1.45 (0.20), residues: 1956 helix: 1.93 (0.15), residues: 1296 sheet: -3.39 (0.35), residues: 96 loop : -0.47 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 420 TYR 0.026 0.001 TYR A 511 PHE 0.027 0.001 PHE C 742 TRP 0.023 0.002 TRP C 372 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00463 (15900) covalent geometry : angle 0.61369 (21556) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.42629 ( 8) hydrogen bonds : bond 0.03609 ( 1013) hydrogen bonds : angle 3.93249 ( 2943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.07 seconds wall clock time: 53 minutes 41.59 seconds (3221.59 seconds total)