Starting phenix.real_space_refine on Mon Aug 10 09:54:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.map" model { file = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2026/8u61_41940.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 104 5.16 5 C 14717 2.51 5 N 3914 2.21 5 O 4304 1.98 5 H 22866 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45921 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 11430 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 bond proxies already assigned to first conformer: 11575 Chain: "B" Number of atoms: 11430 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 bond proxies already assigned to first conformer: 11575 Chain: "A" Number of atoms: 11320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11320 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 50, 'TRANS': 646} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 11229 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 11368 Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 512 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 12.56, per 1000 atoms: 0.27 Number of scatterers: 45921 At special positions: 0 Unit cell: (143.15, 140.696, 179.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 16 15.00 O 4304 8.00 N 3914 7.00 C 14717 6.00 H 22866 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5338 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 17 sheets defined 20.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 114 through 120 removed outlier: 4.131A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'D' and resid 524 through 529 removed outlier: 4.690A pdb=" N LEU D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 542 removed outlier: 3.699A pdb=" N LEU D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.815A pdb=" N ILE D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 713 No H-bonds generated for 'chain 'D' and resid 711 through 713' Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 773 through 780 Processing helix chain 'D' and resid 807 through 822 removed outlier: 3.821A pdb=" N LEU D 822 " --> pdb=" O ALA D 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 114 through 120 removed outlier: 4.130A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.690A pdb=" N LEU B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 542 removed outlier: 3.699A pdb=" N LEU B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.815A pdb=" N ILE B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 773 through 780 Processing helix chain 'B' and resid 807 through 822 removed outlier: 3.820A pdb=" N LEU B 822 " --> pdb=" O ALA B 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.866A pdb=" N ASP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.930A pdb=" N LYS A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.818A pdb=" N SER A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 6.339A pdb=" N GLU A 526 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 528 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 542 removed outlier: 3.588A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.775A pdb=" N ILE A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.815A pdb=" N PHE A 742 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 809 through 822 removed outlier: 3.623A pdb=" N LEU A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.546A pdb=" N THR C 477 " --> pdb=" O GLN C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 534 through 542 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 711 through 714 Processing helix chain 'C' and resid 715 through 722 removed outlier: 3.736A pdb=" N TYR C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 807 through 822 removed outlier: 4.498A pdb=" N GLY C 813 " --> pdb=" O ARG C 809 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE C 816 " --> pdb=" O ALA C 812 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 822 " --> pdb=" O ALA C 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 5.593A pdb=" N VAL D 71 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER D 100 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA D 73 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR D 95 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE D 150 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR D 109 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN D 152 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG D 133 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 153 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 131 " --> pdb=" O VAL D 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 237 through 244 current: chain 'D' and resid 261 through 269 removed outlier: 3.520A pdb=" N GLY D 272 " --> pdb=" O ASP D 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 272 through 278 current: chain 'D' and resid 322 through 330 Processing sheet with id=AA3, first strand: chain 'D' and resid 360 through 361 removed outlier: 4.534A pdb=" N ILE D 378 " --> pdb=" O THR D 361 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 375 through 384 current: chain 'D' and resid 399 through 408 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 416 through 421 current: chain 'D' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 455 through 460 current: chain 'D' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'D' and resid 547 through 561 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 679 through 681 current: chain 'D' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 762 through 768 current: chain 'D' and resid 841 through 849 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 129 removed outlier: 5.594A pdb=" N VAL B 71 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER B 100 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 73 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR B 95 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE B 150 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 109 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN B 152 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 133 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 153 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 131 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 237 through 244 current: chain 'B' and resid 261 through 269 removed outlier: 3.520A pdb=" N GLY B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 272 through 278 current: chain 'B' and resid 322 through 330 Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 361 removed outlier: 4.533A pdb=" N ILE B 378 " --> pdb=" O THR B 361 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 399 through 408 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 416 through 421 current: chain 'B' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 455 through 460 current: chain 'B' and resid 708 through 709 Processing sheet with id=AA8, first strand: chain 'B' and resid 547 through 561 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 679 through 681 current: chain 'B' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 762 through 768 current: chain 'B' and resid 841 through 849 Processing sheet with id=AA9, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.309A pdb=" N THR A 98 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 74 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP A 96 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG A 76 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 94 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR A 95 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N LEU A 148 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 107 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE A 150 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 109 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASN A 152 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 133 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 153 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 131 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 244 current: chain 'A' and resid 261 through 269 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 272 through 278 current: chain 'A' and resid 322 through 327 Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.592A pdb=" N ILE A 378 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS A 406 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 384 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 404 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A 386 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 402 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN A 388 " --> pdb=" O TRP A 400 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A 400 " --> pdb=" O GLN A 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 416 through 421 current: chain 'A' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 455 through 460 current: chain 'A' and resid 708 through 709 Processing sheet with id=AB3, first strand: chain 'A' and resid 547 through 562 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 679 through 681 current: chain 'A' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 762 through 768 current: chain 'A' and resid 841 through 849 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 100 removed outlier: 4.157A pdb=" N ALA C 73 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER C 100 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL C 71 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.378A pdb=" N TYR C 109 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN C 152 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG C 133 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 239 through 244 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 239 through 244 current: chain 'C' and resid 261 through 268 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 384 removed outlier: 6.180A pdb=" N HIS C 406 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL C 384 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP C 404 " --> pdb=" O VAL C 384 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 421 current: chain 'C' and resid 457 through 460 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 457 through 460 current: chain 'C' and resid 708 through 709 Processing sheet with id=AB8, first strand: chain 'C' and resid 679 through 681 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 679 through 681 current: chain 'C' and resid 767 through 768 removed outlier: 7.213A pdb=" N ALA C 767 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS C 847 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS C 840 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 830 " --> pdb=" O HIS C 846 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE C 848 " --> pdb=" O VAL C 828 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL C 828 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 827 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 550 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR C 754 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 762 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP C 694 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASP C 765 " --> pdb=" O ASP C 694 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 696 " --> pdb=" O ASP C 765 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1119 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: 12.00 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22789 1.03 - 1.23: 104 1.23 - 1.42: 9809 1.42 - 1.61: 13679 1.61 - 1.81: 152 Bond restraints: 46533 Sorted by residual: bond pdb=" N HIS B 564 " pdb=" H HIS B 564 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.70e+01 bond pdb=" N SER B 565 " pdb=" H SER B 565 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N SER B 566 " pdb=" H SER B 566 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" NE2 HIS B 564 " pdb=" HE2 HIS B 564 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" CE1 HIS B 564 " pdb=" HE1 HIS B 564 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.81e+01 ... (remaining 46528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 83672 1.89 - 3.78: 650 3.78 - 5.66: 34 5.66 - 7.55: 0 7.55 - 9.44: 2 Bond angle restraints: 84358 Sorted by residual: angle pdb=" CB GLU D 350 " pdb=" CG GLU D 350 " pdb=" CD GLU D 350 " ideal model delta sigma weight residual 112.60 122.04 -9.44 1.70e+00 3.46e-01 3.08e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 12 " pdb=" C4 DT E 12 " pdb=" O4 DT E 12 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E 2 " pdb=" C4 DT E 2 " pdb=" O4 DT E 2 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT E 11 " pdb=" C4 DT E 11 " pdb=" O4 DT E 11 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 84353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 21251 32.24 - 64.48: 644 64.48 - 96.72: 23 96.72 - 128.96: 0 128.96 - 161.20: 1 Dihedral angle restraints: 21919 sinusoidal: 12167 harmonic: 9752 Sorted by residual: dihedral pdb=" C4' DT E 5 " pdb=" C3' DT E 5 " pdb=" O3' DT E 5 " pdb=" P DT E 6 " ideal model delta sinusoidal sigma weight residual 220.00 58.80 161.20 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ASP C 409 " pdb=" CB ASP C 409 " pdb=" CG ASP C 409 " pdb=" OD1 ASP C 409 " ideal model delta sinusoidal sigma weight residual -30.00 -88.53 58.53 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU B 842 " pdb=" CG GLU B 842 " pdb=" CD GLU B 842 " pdb=" OE1 GLU B 842 " ideal model delta sinusoidal sigma weight residual 0.00 89.09 -89.09 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 21916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2342 0.034 - 0.068: 748 0.068 - 0.102: 262 0.102 - 0.136: 170 0.136 - 0.170: 16 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C3' DT E 5 " pdb=" C4' DT E 5 " pdb=" O3' DT E 5 " pdb=" C2' DT E 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C3' DT E 13 " pdb=" C4' DT E 13 " pdb=" O3' DT E 13 " pdb=" C2' DT E 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" C3' DT E 7 " pdb=" C4' DT E 7 " pdb=" O3' DT E 7 " pdb=" C2' DT E 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 3535 not shown) Planarity restraints: 6659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 759 " -0.100 2.00e-02 2.50e+03 1.05e-01 1.66e+02 pdb=" CG ASN C 759 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C 759 " 0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN C 759 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 759 " 0.152 2.00e-02 2.50e+03 pdb="HD22 ASN C 759 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 350 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" N TRP D 351 " 0.037 2.00e-02 2.50e+03 pdb=" CA TRP D 351 " -0.009 2.00e-02 2.50e+03 pdb=" H TRP D 351 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 207 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 208 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.022 5.00e-02 4.00e+02 ... (remaining 6656 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 46 1.75 - 2.46: 31230 2.46 - 3.18: 145545 3.18 - 3.89: 190656 3.89 - 4.60: 302669 Nonbonded interactions: 670146 Sorted by model distance: nonbonded pdb=" HD3 LYS D 348 " pdb=" HD2 PHE A 690 " model vdw 1.039 2.270 nonbonded pdb="HG12 ILE D 143 " pdb="HE22 GLN C 553 " model vdw 1.501 2.270 nonbonded pdb=" O VAL C 384 " pdb=" H GLY C 504 " model vdw 1.584 2.450 nonbonded pdb=" O PRO D 513 " pdb=" HH TYR D 849 " model vdw 1.626 2.450 nonbonded pdb=" O PRO B 513 " pdb=" HH TYR B 849 " model vdw 1.627 2.450 ... (remaining 670141 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 43 through 154 or resid 156 through 564 or (resid 565 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 676 through 682 or (resid 683 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and (name N \ or name CA or name C or name O )) or (resid 692 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 \ or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or n \ ame HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 761 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 762 through 825 or (resid 826 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'B' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 564 or (resid 5 \ 65 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 676 through 682 or (resid 683 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and \ (name N or name CA or name C or name O )) or (resid 692 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 76 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 762 through 825 or (resid 826 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'C' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 851)) selection = (chain 'D' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 564 or (resid 5 \ 65 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 676 through 682 or (resid 683 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and \ (name N or name CA or name C or name O )) or (resid 692 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 76 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 762 through 825 or (resid 826 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 827 through 851)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.580 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: 0.330 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.140 Process input model: 49.250 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4088 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 : 0.003 0.043 23667 Z= 0.171 Angle : 0.582 9.441 32214 Z= 0.359 Chirality : 0.044 0.170 3538 Planarity : 0.004 0.040 4081 Dihedral : 14.014 161.201 9048 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.62 % Allowed : 12.22 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2769 helix: 0.43 (0.26), residues: 409 sheet: -1.60 (0.19), residues: 734 loop : -0.91 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.014 0.001 TYR B 509 PHE 0.007 0.001 PHE A 416 TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (23667) covalent geometry : angle 0.58157 / 0.36 (32214) hydrogen bonds : bond 0.19657 / 13.31 ( 416) hydrogen bonds : angle 8.37823 / 6.00 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 611 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 595 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7120 (t) REVERT: D 141 LYS cc_start: 0.7535 (mmmt) cc_final: 0.7138 (mmmt) REVERT: D 226 MET cc_start: 0.5258 (mmp) cc_final: 0.4889 (mmm) REVERT: D 407 ILE cc_start: 0.5633 (mt) cc_final: 0.5252 (mp) REVERT: B 103 VAL cc_start: 0.5473 (OUTLIER) cc_final: 0.5261 (t) REVERT: A 535 VAL cc_start: 0.8179 (t) cc_final: 0.7834 (t) REVERT: C 241 ILE cc_start: 0.4793 (mt) cc_final: 0.4357 (mt) REVERT: C 431 ASN cc_start: 0.8111 (m-40) cc_final: 0.6956 (t0) REVERT: C 782 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8189 (tp) outliers start: 16 outliers final: 4 residues processed: 610 average time/residue: 0.4394 time to fit residues: 398.3649 Evaluate side-chains 364 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 357 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 283 CYS Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain C residue 782 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 223 HIS D 448 ASN D 750 HIS B 120 GLN B 212 ASN B 388 GLN B 760 HIS B 846 HIS A 487 GLN A 553 GLN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 ASN ** C 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.105306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.087363 restraints weight = 347499.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.090544 restraints weight = 169271.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.092552 restraints weight = 98888.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.093780 restraints weight = 66407.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.094475 restraints weight = 50250.399| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4262 r_free = 0.4262 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23667 Z= 0.190 Angle : 0.647 6.785 32214 Z= 0.338 Chirality : 0.046 0.172 3538 Planarity : 0.005 0.061 4081 Dihedral : 8.644 160.729 3256 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.86 % Allowed : 17.38 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2769 helix: 0.25 (0.25), residues: 417 sheet: -1.78 (0.18), residues: 758 loop : -0.94 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 447 TYR 0.028 0.002 TYR D 795 PHE 0.019 0.002 PHE D 438 TRP 0.037 0.002 TRP C 228 HIS 0.025 0.001 HIS C 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (23667) covalent geometry : angle 0.64685 / 0.34 (32214) hydrogen bonds : bond 0.04408 / 3.07 ( 416) hydrogen bonds : angle 6.74815 / 4.83 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 355 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7823 (mmmt) REVERT: D 384 VAL cc_start: 0.6846 (t) cc_final: 0.6625 (t) REVERT: A 330 LEU cc_start: 0.8236 (mp) cc_final: 0.7969 (mm) REVERT: A 332 LEU cc_start: 0.5306 (OUTLIER) cc_final: 0.4914 (pp) REVERT: A 335 PRO cc_start: 0.5513 (Cg_endo) cc_final: 0.5268 (Cg_exo) REVERT: C 381 LEU cc_start: 0.6691 (mt) cc_final: 0.6465 (mp) REVERT: C 833 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7682 (mt) outliers start: 48 outliers final: 29 residues processed: 392 average time/residue: 0.4184 time to fit residues: 248.6648 Evaluate side-chains 326 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 295 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 223 HIS Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 123 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 553 GLN B 697 HIS B 750 HIS B 760 HIS B 797 GLN A 553 GLN A 683 GLN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.100181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.081825 restraints weight = 361231.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.084823 restraints weight = 178849.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.086624 restraints weight = 104953.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.087740 restraints weight = 72336.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.088415 restraints weight = 56157.524| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 23667 Z= 0.250 Angle : 0.709 8.345 32214 Z= 0.378 Chirality : 0.047 0.349 3538 Planarity : 0.006 0.062 4081 Dihedral : 8.917 160.255 3247 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.64 % Allowed : 17.53 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2769 helix: -0.15 (0.24), residues: 415 sheet: -2.10 (0.18), residues: 800 loop : -1.21 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 472 TYR 0.025 0.003 TYR B 722 PHE 0.060 0.002 PHE C 710 TRP 0.023 0.002 TRP C 45 HIS 0.064 0.003 HIS D 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 (23667) covalent geometry : angle 0.70850 / 0.38 (32214) hydrogen bonds : bond 0.04642 / 3.26 ( 416) hydrogen bonds : angle 6.73272 / 4.81 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8051 (mmmt) REVERT: D 384 VAL cc_start: 0.6843 (t) cc_final: 0.6591 (t) REVERT: D 416 PHE cc_start: 0.7741 (m-80) cc_final: 0.7148 (m-80) REVERT: D 752 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7894 (tm-30) REVERT: B 246 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6067 (mtmt) REVERT: A 332 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4822 (pp) REVERT: C 101 ASP cc_start: 0.3459 (OUTLIER) cc_final: 0.3204 (m-30) REVERT: C 265 LEU cc_start: 0.8570 (mp) cc_final: 0.8127 (tp) REVERT: C 358 HIS cc_start: 0.6888 (m-70) cc_final: 0.6473 (m-70) REVERT: C 833 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7837 (mt) outliers start: 68 outliers final: 42 residues processed: 340 average time/residue: 0.3781 time to fit residues: 200.2513 Evaluate side-chains 303 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 27 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 268 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 750 HIS B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 760 HIS ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.100492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.082336 restraints weight = 363666.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.085208 restraints weight = 181412.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.086950 restraints weight = 109302.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.088001 restraints weight = 76256.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.088621 restraints weight = 59793.220| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23667 Z= 0.150 Angle : 0.602 7.517 32214 Z= 0.312 Chirality : 0.045 0.159 3538 Planarity : 0.005 0.058 4081 Dihedral : 8.815 159.213 3247 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.06 % Allowed : 18.50 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2769 helix: 0.16 (0.25), residues: 417 sheet: -2.10 (0.18), residues: 794 loop : -1.12 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.018 0.002 TYR D 561 PHE 0.023 0.001 PHE C 710 TRP 0.022 0.001 TRP B 400 HIS 0.012 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (23667) covalent geometry : angle 0.60221 / 0.31 (32214) hydrogen bonds : bond 0.03458 / 2.42 ( 416) hydrogen bonds : angle 6.29121 / 4.50 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 ILE cc_start: 0.8786 (mt) cc_final: 0.8181 (mt) REVERT: D 384 VAL cc_start: 0.6728 (t) cc_final: 0.6458 (t) REVERT: D 416 PHE cc_start: 0.7749 (m-80) cc_final: 0.7209 (m-80) REVERT: D 751 PHE cc_start: 0.8032 (m-80) cc_final: 0.7146 (m-80) REVERT: D 805 LEU cc_start: 0.5867 (mm) cc_final: 0.5664 (mm) REVERT: B 246 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6170 (mtmt) REVERT: B 705 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7277 (p) REVERT: B 797 GLN cc_start: 0.2415 (OUTLIER) cc_final: 0.2207 (mt0) REVERT: A 326 MET cc_start: 0.6388 (ppp) cc_final: 0.5903 (tmm) REVERT: A 332 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4874 (pp) REVERT: C 833 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7863 (mt) outliers start: 53 outliers final: 39 residues processed: 308 average time/residue: 0.3591 time to fit residues: 172.4349 Evaluate side-chains 292 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 247 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 270 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 HIS ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.101069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.082555 restraints weight = 362430.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.085630 restraints weight = 174145.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.087510 restraints weight = 102277.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.088647 restraints weight = 69757.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.089356 restraints weight = 53962.542| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23667 Z= 0.112 Angle : 0.569 5.613 32214 Z= 0.293 Chirality : 0.045 0.177 3538 Planarity : 0.004 0.055 4081 Dihedral : 8.710 159.550 3247 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.75 % Allowed : 19.08 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2769 helix: 0.38 (0.25), residues: 417 sheet: -1.97 (0.18), residues: 778 loop : -1.01 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.013 0.001 TYR C 509 PHE 0.019 0.001 PHE C 710 TRP 0.016 0.001 TRP C 45 HIS 0.010 0.001 HIS D 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (23667) covalent geometry : angle 0.56890 / 0.29 (32214) hydrogen bonds : bond 0.03254 / 2.27 ( 416) hydrogen bonds : angle 6.09468 / 4.35 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 384 VAL cc_start: 0.6637 (t) cc_final: 0.6372 (t) REVERT: D 416 PHE cc_start: 0.7669 (m-80) cc_final: 0.7112 (m-80) REVERT: D 750 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: D 751 PHE cc_start: 0.7794 (m-80) cc_final: 0.6649 (m-80) REVERT: B 705 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7142 (p) REVERT: A 326 MET cc_start: 0.6354 (ppp) cc_final: 0.5809 (tmm) REVERT: A 332 LEU cc_start: 0.5239 (OUTLIER) cc_final: 0.4846 (pp) REVERT: C 101 ASP cc_start: 0.3590 (OUTLIER) cc_final: 0.3227 (m-30) REVERT: C 265 LEU cc_start: 0.8598 (mt) cc_final: 0.8191 (tp) REVERT: C 833 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7799 (mt) outliers start: 45 outliers final: 34 residues processed: 296 average time/residue: 0.3429 time to fit residues: 156.6175 Evaluate side-chains 284 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 186 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 82 optimal weight: 0.3980 chunk 200 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 750 HIS B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.099773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.081992 restraints weight = 363596.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.084560 restraints weight = 179399.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.085660 restraints weight = 106937.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085972 restraints weight = 102599.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.086161 restraints weight = 98751.451| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23667 Z= 0.144 Angle : 0.575 8.095 32214 Z= 0.298 Chirality : 0.044 0.186 3538 Planarity : 0.004 0.060 4081 Dihedral : 8.719 160.251 3246 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 1.82 % Allowed : 19.08 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2769 helix: 0.33 (0.25), residues: 429 sheet: -2.04 (0.18), residues: 769 loop : -1.04 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.011 0.001 TYR D 561 PHE 0.015 0.001 PHE C 710 TRP 0.030 0.001 TRP B 400 HIS 0.027 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (23667) covalent geometry : angle 0.57518 / 0.30 (32214) hydrogen bonds : bond 0.03232 / 2.25 ( 416) hydrogen bonds : angle 6.10190 / 4.35 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 LEU cc_start: 0.8897 (tp) cc_final: 0.8633 (tp) REVERT: D 384 VAL cc_start: 0.6661 (t) cc_final: 0.6395 (t) REVERT: D 416 PHE cc_start: 0.7730 (m-80) cc_final: 0.7148 (m-80) REVERT: D 751 PHE cc_start: 0.7770 (m-80) cc_final: 0.6902 (m-80) REVERT: D 805 LEU cc_start: 0.5770 (mm) cc_final: 0.5555 (mm) REVERT: B 93 TYR cc_start: 0.7903 (m-80) cc_final: 0.7206 (m-80) REVERT: A 326 MET cc_start: 0.6613 (ppp) cc_final: 0.6094 (tmm) REVERT: A 332 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5044 (pp) REVERT: A 357 ASN cc_start: 0.4441 (OUTLIER) cc_final: 0.3880 (t0) REVERT: C 101 ASP cc_start: 0.3539 (OUTLIER) cc_final: 0.3189 (m-30) REVERT: C 265 LEU cc_start: 0.8566 (mt) cc_final: 0.8363 (mt) REVERT: C 833 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7830 (mt) outliers start: 47 outliers final: 35 residues processed: 285 average time/residue: 0.3063 time to fit residues: 136.7330 Evaluate side-chains 279 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 273 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 258 optimal weight: 0.0870 chunk 270 optimal weight: 0.7980 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 331 ASN B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 HIS ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.098662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.080880 restraints weight = 364038.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.083852 restraints weight = 183219.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.084307 restraints weight = 105250.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.085885 restraints weight = 95194.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.085734 restraints weight = 91961.498| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23667 Z= 0.159 Angle : 0.582 5.556 32214 Z= 0.303 Chirality : 0.045 0.281 3538 Planarity : 0.005 0.054 4081 Dihedral : 8.775 160.185 3246 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 2.06 % Allowed : 18.85 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.16), residues: 2769 helix: 0.18 (0.25), residues: 441 sheet: -2.07 (0.18), residues: 754 loop : -1.10 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 142 TYR 0.012 0.002 TYR B 188 PHE 0.029 0.002 PHE D 768 TRP 0.025 0.001 TRP B 400 HIS 0.031 0.001 HIS D 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (23667) covalent geometry : angle 0.58203 / 0.30 (32214) hydrogen bonds : bond 0.03183 / 2.23 ( 416) hydrogen bonds : angle 6.04235 / 4.32 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 384 VAL cc_start: 0.6608 (t) cc_final: 0.6349 (t) REVERT: D 751 PHE cc_start: 0.7466 (m-80) cc_final: 0.6554 (m-80) REVERT: B 93 TYR cc_start: 0.8027 (m-80) cc_final: 0.7379 (m-80) REVERT: A 326 MET cc_start: 0.6663 (ppp) cc_final: 0.6135 (tmm) REVERT: A 332 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5041 (pp) REVERT: C 101 ASP cc_start: 0.3616 (OUTLIER) cc_final: 0.3264 (m-30) REVERT: C 833 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7970 (mt) outliers start: 53 outliers final: 36 residues processed: 282 average time/residue: 0.3272 time to fit residues: 142.9672 Evaluate side-chains 271 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 210 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 HIS D 838 ASN B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.096108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.077907 restraints weight = 375202.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.080351 restraints weight = 190471.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.081793 restraints weight = 116222.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.082964 restraints weight = 83913.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.083615 restraints weight = 65778.033| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23667 Z= 0.227 Angle : 0.658 7.764 32214 Z= 0.346 Chirality : 0.046 0.304 3538 Planarity : 0.006 0.072 4081 Dihedral : 9.003 159.714 3246 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.34 % Favored : 91.62 % Rotamer: Outliers : 2.21 % Allowed : 18.77 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2769 helix: -0.19 (0.25), residues: 443 sheet: -2.29 (0.18), residues: 764 loop : -1.35 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.039 0.002 TYR D 509 PHE 0.019 0.002 PHE C 751 TRP 0.021 0.002 TRP B 680 HIS 0.075 0.002 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (23667) covalent geometry : angle 0.65830 / 0.35 (32214) hydrogen bonds : bond 0.03630 / 2.54 ( 416) hydrogen bonds : angle 6.28907 / 4.51 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 384 VAL cc_start: 0.6613 (t) cc_final: 0.6352 (t) REVERT: D 507 TYR cc_start: 0.8130 (t80) cc_final: 0.7445 (t80) REVERT: B 93 TYR cc_start: 0.8190 (m-80) cc_final: 0.7585 (m-80) REVERT: A 326 MET cc_start: 0.6939 (ppp) cc_final: 0.6436 (tmm) REVERT: A 332 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5032 (pp) REVERT: A 357 ASN cc_start: 0.4416 (OUTLIER) cc_final: 0.3633 (t0) REVERT: C 101 ASP cc_start: 0.3769 (OUTLIER) cc_final: 0.3530 (m-30) outliers start: 57 outliers final: 44 residues processed: 286 average time/residue: 0.3322 time to fit residues: 147.7343 Evaluate side-chains 279 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.096651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.078193 restraints weight = 364378.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.080940 restraints weight = 183253.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.082557 restraints weight = 110389.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.083612 restraints weight = 77874.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.084214 restraints weight = 61478.856| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 23667 Z= 0.156 Angle : 0.607 7.655 32214 Z= 0.314 Chirality : 0.045 0.173 3538 Planarity : 0.005 0.051 4081 Dihedral : 8.955 159.163 3246 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 1.86 % Allowed : 19.24 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.16), residues: 2769 helix: -0.03 (0.25), residues: 441 sheet: -2.34 (0.18), residues: 768 loop : -1.23 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 778 TYR 0.045 0.002 TYR D 509 PHE 0.041 0.002 PHE D 751 TRP 0.029 0.002 TRP C 45 HIS 0.022 0.001 HIS D 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (23667) covalent geometry : angle 0.60709 / 0.31 (32214) hydrogen bonds : bond 0.03245 / 2.26 ( 416) hydrogen bonds : angle 6.09591 / 4.36 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 376 ASP cc_start: 0.6771 (t70) cc_final: 0.6562 (t70) REVERT: D 384 VAL cc_start: 0.6430 (t) cc_final: 0.6168 (t) REVERT: D 507 TYR cc_start: 0.7684 (t80) cc_final: 0.7451 (t80) REVERT: D 751 PHE cc_start: 0.7936 (m-80) cc_final: 0.7172 (m-80) REVERT: B 403 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6530 (ptp-110) REVERT: A 326 MET cc_start: 0.6863 (ppp) cc_final: 0.6368 (tmm) REVERT: A 332 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.5113 (pp) REVERT: C 101 ASP cc_start: 0.3804 (OUTLIER) cc_final: 0.3145 (m-30) REVERT: C 786 LEU cc_start: 0.7666 (mt) cc_final: 0.7423 (mt) outliers start: 48 outliers final: 42 residues processed: 271 average time/residue: 0.3965 time to fit residues: 166.4218 Evaluate side-chains 275 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 115 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 266 optimal weight: 0.0030 chunk 130 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 838 ASN B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.097824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.079651 restraints weight = 364331.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.082312 restraints weight = 181906.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.084023 restraints weight = 107983.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.085041 restraints weight = 75269.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.085670 restraints weight = 58975.578| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23667 Z= 0.110 Angle : 0.570 6.142 32214 Z= 0.290 Chirality : 0.045 0.179 3538 Planarity : 0.005 0.052 4081 Dihedral : 8.820 159.536 3246 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 1.16 % Allowed : 19.94 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.16), residues: 2769 helix: 0.28 (0.26), residues: 441 sheet: -2.21 (0.18), residues: 735 loop : -1.07 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 76 TYR 0.034 0.001 TYR D 509 PHE 0.034 0.001 PHE B 467 TRP 0.034 0.001 TRP C 45 HIS 0.015 0.001 HIS D 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (23667) covalent geometry : angle 0.57005 / 0.29 (32214) hydrogen bonds : bond 0.02909 / 2.00 ( 416) hydrogen bonds : angle 5.83543 / 4.18 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 376 ASP cc_start: 0.6546 (t70) cc_final: 0.6282 (t70) REVERT: D 384 VAL cc_start: 0.6270 (t) cc_final: 0.6001 (t) REVERT: D 751 PHE cc_start: 0.7969 (m-80) cc_final: 0.7084 (m-80) REVERT: B 246 LYS cc_start: 0.6952 (mtmt) cc_final: 0.6729 (mtmm) REVERT: B 403 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6419 (ptp-110) REVERT: A 326 MET cc_start: 0.6720 (ppp) cc_final: 0.6248 (tmm) REVERT: A 332 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5083 (pp) REVERT: C 786 LEU cc_start: 0.7682 (mt) cc_final: 0.7468 (mt) outliers start: 30 outliers final: 24 residues processed: 269 average time/residue: 0.2940 time to fit residues: 122.4170 Evaluate side-chains 264 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS C 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.095602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077038 restraints weight = 374372.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079674 restraints weight = 184447.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.081384 restraints weight = 111619.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.082255 restraints weight = 78140.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.082678 restraints weight = 63327.350| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23667 Z= 0.188 Angle : 0.626 11.461 32214 Z= 0.325 Chirality : 0.045 0.172 3538 Planarity : 0.005 0.060 4081 Dihedral : 8.933 160.489 3246 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.23 % Favored : 91.73 % Rotamer: Outliers : 1.36 % Allowed : 19.98 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.16), residues: 2769 helix: 0.06 (0.25), residues: 442 sheet: -2.42 (0.18), residues: 748 loop : -1.22 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 778 TYR 0.038 0.002 TYR D 509 PHE 0.044 0.002 PHE B 751 TRP 0.019 0.002 TRP D 228 HIS 0.009 0.001 HIS B 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (23667) covalent geometry : angle 0.62637 / 0.32 (32214) hydrogen bonds : bond 0.03371 / 2.33 ( 416) hydrogen bonds : angle 6.07468 / 4.37 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8225.97 seconds wall clock time: 141 minutes 0.20 seconds (8460.20 seconds total)