Starting phenix.real_space_refine on Tue Jul 7 07:33:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u61_41940/07_2026/8u61_41940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u61_41940/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u61_41940/07_2026/8u61_41940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u61_41940/07_2026/8u61_41940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u61_41940/07_2026/8u61_41940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u61_41940/07_2026/8u61_41940.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 10.88, per 1000 atoms: 0.24 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: 4.28 Conformation dependent library (CDL) restraints added in 1.9 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: 0.77 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: 11.84 Time building geometry restraints manager: 5.90 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: 12.520 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: 0.200 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 46.920 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.870 ------------------------------------------------------------------------------- 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 : 0.581 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 0.58138 / 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 : 1.210 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: 0.7119 (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: 0.4890 (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: 0.5257 (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: 0.4358 (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: 0.8190 (tp) outliers start: 16 outliers final: 4 residues processed: 610 average time/residue: 0.4269 time to fit residues: 386.6024 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 : 1.165 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.105456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.087492 restraints weight = 347046.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.090696 restraints weight = 169355.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.092714 restraints weight = 98719.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.093909 restraints weight = 66163.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.094631 restraints weight = 50230.289| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4266 r_free = 0.4266 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 = 0.4266 r_free = 0.4266 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: 0.4266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23667 Z= 0.191 Angle : 0.635 7.130 32214 Z= 0.332 Chirality : 0.046 0.168 3538 Planarity : 0.005 0.064 4081 Dihedral : 8.614 160.669 3256 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.75 % Allowed : 17.53 % Favored : 80.72 % 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: -1.53 (0.16), residues: 2769 helix: 0.28 (0.25), residues: 417 sheet: -1.77 (0.18), residues: 758 loop : -0.92 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 447 TYR 0.030 0.002 TYR D 287 PHE 0.013 0.001 PHE A 690 TRP 0.019 0.002 TRP B 400 HIS 0.007 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (23667) covalent geometry : angle 0.63484 / 0.33 (32214) hydrogen bonds : bond 0.04904 / 3.36 ( 416) hydrogen bonds : angle 6.79414 / 4.86 ( 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 399 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 354 time to evaluate : 1.281 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: D 141 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7795 (mmmt) REVERT: D 384 VAL cc_start: 0.6888 (t) cc_final: 0.6652 (t) REVERT: A 332 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4737 (pp) REVERT: C 381 LEU cc_start: 0.6626 (mt) cc_final: 0.6424 (mp) REVERT: C 833 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7717 (mt) outliers start: 45 outliers final: 28 residues processed: 390 average time/residue: 0.4086 time to fit residues: 240.1157 Evaluate side-chains 321 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 127 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 838 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 448 ASN B 553 GLN ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4396 r_free = 0.4396 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.081345 restraints weight = 368347.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.084067 restraints weight = 187009.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085815 restraints weight = 112934.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.086854 restraints weight = 78575.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.087454 restraints weight = 62035.122| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 23667 Z= 0.293 Angle : 0.773 10.485 32214 Z= 0.415 Chirality : 0.049 0.326 3538 Planarity : 0.007 0.062 4081 Dihedral : 9.079 160.031 3247 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.70 % Rotamer: Outliers : 3.10 % Allowed : 17.42 % Favored : 79.48 % 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: -2.24 (0.15), residues: 2769 helix: -0.36 (0.24), residues: 415 sheet: -2.15 (0.18), residues: 794 loop : -1.39 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 549 TYR 0.031 0.003 TYR C 287 PHE 0.050 0.003 PHE C 710 TRP 0.024 0.002 TRP C 45 HIS 0.056 0.003 HIS D 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (23667) covalent geometry : angle 0.77307 / 0.42 (32214) hydrogen bonds : bond 0.05012 / 3.54 ( 416) hydrogen bonds : angle 6.94152 / 4.96 ( 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 371 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 1.120 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: D 141 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8242 (mmmt) REVERT: D 366 LEU cc_start: 0.8881 (tp) cc_final: 0.8665 (tp) REVERT: D 374 ILE cc_start: 0.8930 (mt) cc_final: 0.8399 (mt) REVERT: D 384 VAL cc_start: 0.6731 (t) cc_final: 0.6461 (t) REVERT: D 416 PHE cc_start: 0.7889 (m-80) cc_final: 0.7286 (m-80) REVERT: D 751 PHE cc_start: 0.7831 (m-80) cc_final: 0.7215 (m-80) REVERT: D 752 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7874 (tm-30) REVERT: B 246 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6224 (mtmt) REVERT: A 332 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4723 (pp) REVERT: C 101 ASP cc_start: 0.3465 (OUTLIER) cc_final: 0.3221 (m-30) REVERT: C 265 LEU cc_start: 0.8720 (mp) cc_final: 0.8332 (tp) REVERT: C 830 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 833 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7940 (mt) outliers start: 80 outliers final: 52 residues processed: 348 average time/residue: 0.3577 time to fit residues: 193.6927 Evaluate side-chains 310 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 540 GLU 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 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 277 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 298 LEU 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 225 GLU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 326 MET 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 405 ILE 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 719 SER Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 830 ILE 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: 0.0970 chunk 186 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 HIS D 838 ASN B 120 GLN B 212 ASN B 312 GLN B 697 HIS B 760 HIS ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.100939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.083341 restraints weight = 360490.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.085952 restraints weight = 182788.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.087179 restraints weight = 104733.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.087304 restraints weight = 94745.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.087379 restraints weight = 87277.314| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23667 Z= 0.124 Angle : 0.591 6.406 32214 Z= 0.306 Chirality : 0.045 0.160 3538 Planarity : 0.005 0.057 4081 Dihedral : 8.826 158.880 3247 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.02 % Allowed : 18.81 % 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: -1.86 (0.16), residues: 2769 helix: 0.18 (0.25), residues: 417 sheet: -2.02 (0.18), residues: 778 loop : -1.15 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.016 0.001 TYR C 795 PHE 0.020 0.001 PHE C 710 TRP 0.016 0.001 TRP D 228 HIS 0.011 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (23667) covalent geometry : angle 0.59102 / 0.31 (32214) hydrogen bonds : bond 0.03389 / 2.37 ( 416) hydrogen bonds : angle 6.26454 / 4.49 ( 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 320 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 1.045 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: D 326 MET cc_start: 0.7457 (ttm) cc_final: 0.7099 (ttm) REVERT: D 366 LEU cc_start: 0.8844 (tp) cc_final: 0.8599 (tp) REVERT: D 384 VAL cc_start: 0.6712 (t) cc_final: 0.6444 (t) REVERT: D 416 PHE cc_start: 0.7765 (m-80) cc_final: 0.7240 (m-80) REVERT: D 428 ILE cc_start: 0.8736 (mm) cc_final: 0.8522 (mm) REVERT: B 246 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6174 (mtmt) REVERT: B 705 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 326 MET cc_start: 0.6377 (ppp) cc_final: 0.5848 (tmm) REVERT: A 332 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4803 (pp) REVERT: C 833 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7837 (mt) outliers start: 52 outliers final: 38 residues processed: 301 average time/residue: 0.3396 time to fit residues: 157.9555 Evaluate side-chains 294 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 750 HIS Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain B residue 131 ILE 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 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 466 VAL 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 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 515 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: 3.9990 chunk 93 optimal weight: 9.9990 chunk 270 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 442 GLN ** D 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 193 ASN B 212 ASN 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 = 0.4407 r_free = 0.4407 target = 0.099872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.081532 restraints weight = 364022.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.084520 restraints weight = 180626.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.086254 restraints weight = 106741.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.087312 restraints weight = 74397.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.087896 restraints weight = 58194.277| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23667 Z= 0.148 Angle : 0.589 6.541 32214 Z= 0.306 Chirality : 0.045 0.156 3538 Planarity : 0.005 0.058 4081 Dihedral : 8.799 159.755 3247 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.02 % Allowed : 19.08 % 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: -1.82 (0.16), residues: 2769 helix: 0.15 (0.25), residues: 429 sheet: -2.09 (0.18), residues: 778 loop : -1.05 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.011 0.002 TYR B 188 PHE 0.018 0.001 PHE C 710 TRP 0.016 0.001 TRP C 45 HIS 0.022 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (23667) covalent geometry : angle 0.58912 / 0.31 (32214) hydrogen bonds : bond 0.03407 / 2.37 ( 416) hydrogen bonds : angle 6.21519 / 4.45 ( 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 308 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 1.060 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: D 366 LEU cc_start: 0.8874 (tp) cc_final: 0.8603 (tp) REVERT: D 384 VAL cc_start: 0.6661 (t) cc_final: 0.6386 (t) REVERT: D 416 PHE cc_start: 0.7647 (m-80) cc_final: 0.7097 (m-80) REVERT: B 193 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.5444 (p0) REVERT: A 326 MET cc_start: 0.6511 (ppp) cc_final: 0.5935 (tmm) REVERT: A 332 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4685 (pp) REVERT: A 357 ASN cc_start: 0.4426 (OUTLIER) cc_final: 0.3915 (t0) REVERT: C 101 ASP cc_start: 0.3492 (OUTLIER) cc_final: 0.3144 (m-30) REVERT: C 833 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7816 (mt) outliers start: 52 outliers final: 38 residues processed: 294 average time/residue: 0.3206 time to fit residues: 146.3125 Evaluate side-chains 292 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 469 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain B residue 193 ASN 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 530 THR 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 797 GLN 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 357 ASN Chi-restraints excluded: chain A residue 466 VAL 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 50 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 405 ILE 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 515 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 186 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 193 ASN B 212 ASN 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 = 0.4398 r_free = 0.4398 target = 0.099412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.081540 restraints weight = 364622.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.084249 restraints weight = 178375.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.085118 restraints weight = 104071.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.085385 restraints weight = 103520.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.085566 restraints weight = 97870.198| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 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 = 0.4056 r_free = 0.4056 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: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23667 Z= 0.143 Angle : 0.577 5.885 32214 Z= 0.300 Chirality : 0.044 0.174 3538 Planarity : 0.005 0.054 4081 Dihedral : 8.802 159.821 3247 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.50 % Rotamer: Outliers : 2.02 % Allowed : 18.93 % Favored : 79.05 % 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: -1.79 (0.16), residues: 2769 helix: 0.19 (0.25), residues: 431 sheet: -2.07 (0.18), residues: 763 loop : -1.05 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.012 0.001 TYR B 844 PHE 0.015 0.001 PHE D 751 TRP 0.016 0.001 TRP C 45 HIS 0.011 0.001 HIS D 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (23667) covalent geometry : angle 0.57741 / 0.30 (32214) hydrogen bonds : bond 0.03243 / 2.26 ( 416) hydrogen bonds : angle 6.15589 / 4.42 ( 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 299 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.266 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: D 366 LEU cc_start: 0.8927 (tp) cc_final: 0.8695 (tp) REVERT: D 384 VAL cc_start: 0.6698 (t) cc_final: 0.6432 (t) REVERT: D 416 PHE cc_start: 0.7708 (m-80) cc_final: 0.7139 (m-80) REVERT: D 751 PHE cc_start: 0.7584 (m-10) cc_final: 0.6927 (m-80) REVERT: B 797 GLN cc_start: 0.2711 (OUTLIER) cc_final: 0.2002 (tm-30) REVERT: A 326 MET cc_start: 0.6629 (ppp) cc_final: 0.6033 (tmm) REVERT: A 332 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4793 (pp) REVERT: C 101 ASP cc_start: 0.3516 (OUTLIER) cc_final: 0.3207 (m-30) REVERT: C 833 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 52 outliers final: 39 residues processed: 282 average time/residue: 0.3158 time to fit residues: 138.3772 Evaluate side-chains 283 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain D residue 469 THR 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 760 HIS Chi-restraints excluded: chain B residue 797 GLN 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 477 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 50 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 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 515 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: 9.9990 chunk 161 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 331 ASN ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.096935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.078626 restraints weight = 367682.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.081342 restraints weight = 187565.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.082903 restraints weight = 113501.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.083928 restraints weight = 80583.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.084520 restraints weight = 63847.213| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 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 = 0.4045 r_free = 0.4045 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: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23667 Z= 0.208 Angle : 0.632 8.345 32214 Z= 0.332 Chirality : 0.045 0.233 3538 Planarity : 0.005 0.052 4081 Dihedral : 8.965 159.822 3246 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.31 % Rotamer: Outliers : 2.25 % Allowed : 18.50 % Favored : 79.25 % 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: -2.12 (0.16), residues: 2769 helix: -0.12 (0.25), residues: 443 sheet: -2.28 (0.18), residues: 740 loop : -1.29 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 746 TYR 0.016 0.002 TYR D 722 PHE 0.014 0.002 PHE B 421 TRP 0.018 0.002 TRP C 45 HIS 0.057 0.002 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (23667) covalent geometry : angle 0.63204 / 0.33 (32214) hydrogen bonds : bond 0.03563 / 2.50 ( 416) hydrogen bonds : angle 6.32315 / 4.55 ( 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 301 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.886 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: D 384 VAL cc_start: 0.6614 (t) cc_final: 0.6348 (t) REVERT: D 751 PHE cc_start: 0.7743 (m-10) cc_final: 0.7029 (m-80) REVERT: B 93 TYR cc_start: 0.8270 (m-80) cc_final: 0.7699 (m-80) REVERT: B 711 MET cc_start: 0.8202 (mtt) cc_final: 0.7425 (mmm) REVERT: A 326 MET cc_start: 0.6703 (ppp) cc_final: 0.6129 (tmm) REVERT: A 332 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4865 (pp) REVERT: A 357 ASN cc_start: 0.4226 (OUTLIER) cc_final: 0.3560 (t0) REVERT: C 101 ASP cc_start: 0.3612 (OUTLIER) cc_final: 0.3324 (m-30) REVERT: C 833 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7964 (mt) outliers start: 58 outliers final: 44 residues processed: 282 average time/residue: 0.3005 time to fit residues: 129.0686 Evaluate side-chains 277 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 469 THR Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain B residue 60 CYS 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 530 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 827 ILE 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 357 ASN 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 686 ARG 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 239 VAL 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 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 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: 3.9990 chunk 26 optimal weight: 0.9990 chunk 193 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 233 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN B 120 GLN B 212 ASN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.098043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.079591 restraints weight = 366358.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.082412 restraints weight = 181355.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.084082 restraints weight = 109488.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.085120 restraints weight = 76306.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.085772 restraints weight = 60214.237| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 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 = 0.4067 r_free = 0.4067 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: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23667 Z= 0.125 Angle : 0.581 7.828 32214 Z= 0.297 Chirality : 0.045 0.243 3538 Planarity : 0.005 0.053 4081 Dihedral : 8.870 159.344 3246 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 1.67 % Allowed : 19.24 % 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: -1.93 (0.16), residues: 2769 helix: 0.07 (0.25), residues: 455 sheet: -2.21 (0.18), residues: 766 loop : -1.13 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.014 0.001 TYR C 307 PHE 0.014 0.001 PHE D 213 TRP 0.020 0.001 TRP C 45 HIS 0.006 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23667) covalent geometry : angle 0.58078 / 0.30 (32214) hydrogen bonds : bond 0.03072 / 2.17 ( 416) hydrogen bonds : angle 6.03908 / 4.34 ( 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 285 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.809 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: D 384 VAL cc_start: 0.6497 (t) cc_final: 0.6237 (t) REVERT: D 751 PHE cc_start: 0.7802 (m-10) cc_final: 0.7096 (m-80) REVERT: B 93 TYR cc_start: 0.8195 (m-80) cc_final: 0.7645 (m-80) REVERT: B 246 LYS cc_start: 0.6863 (mtmt) cc_final: 0.6648 (mtmt) REVERT: B 711 MET cc_start: 0.8045 (mtt) cc_final: 0.7324 (mmm) REVERT: A 326 MET cc_start: 0.6644 (ppp) cc_final: 0.6121 (tmm) REVERT: A 332 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4782 (pp) REVERT: C 786 LEU cc_start: 0.7740 (mt) cc_final: 0.7507 (mt) REVERT: C 833 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7830 (mt) outliers start: 43 outliers final: 35 residues processed: 271 average time/residue: 0.2744 time to fit residues: 113.1477 Evaluate side-chains 272 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 753 VAL 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 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 827 ILE Chi-restraints excluded: chain B residue 833 ILE 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 477 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 239 VAL 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 469 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 501 MET 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 Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.097189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.078678 restraints weight = 366273.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.081355 restraints weight = 182013.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.083112 restraints weight = 110293.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.084130 restraints weight = 76787.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.084762 restraints weight = 60496.627| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 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 = 0.4048 r_free = 0.4048 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: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23667 Z= 0.140 Angle : 0.579 7.456 32214 Z= 0.296 Chirality : 0.045 0.201 3538 Planarity : 0.005 0.051 4081 Dihedral : 8.865 160.282 3246 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 1.55 % Allowed : 19.32 % Favored : 79.13 % 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: -1.93 (0.16), residues: 2769 helix: 0.08 (0.25), residues: 453 sheet: -2.24 (0.18), residues: 766 loop : -1.11 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 490 TYR 0.016 0.002 TYR D 509 PHE 0.017 0.001 PHE C 710 TRP 0.034 0.001 TRP C 45 HIS 0.009 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (23667) covalent geometry : angle 0.57922 / 0.30 (32214) hydrogen bonds : bond 0.03089 / 2.15 ( 416) hydrogen bonds : angle 6.02728 / 4.34 ( 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 281 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.731 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: D 384 VAL cc_start: 0.6310 (t) cc_final: 0.6052 (t) REVERT: D 750 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.8039 (t-90) REVERT: D 751 PHE cc_start: 0.7854 (m-10) cc_final: 0.7078 (m-80) REVERT: B 93 TYR cc_start: 0.8256 (m-80) cc_final: 0.7764 (m-80) REVERT: B 711 MET cc_start: 0.8101 (mtt) cc_final: 0.7363 (mmm) REVERT: A 326 MET cc_start: 0.6709 (ppp) cc_final: 0.6219 (tmm) REVERT: A 332 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.4888 (pp) REVERT: C 786 LEU cc_start: 0.7632 (mt) cc_final: 0.7390 (mt) REVERT: C 833 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7879 (mt) outliers start: 40 outliers final: 33 residues processed: 270 average time/residue: 0.2483 time to fit residues: 102.7932 Evaluate side-chains 269 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain B residue 60 CYS 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 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 477 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 239 VAL 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 469 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 501 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 115 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 266 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- 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 312 GLN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.097603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.079042 restraints weight = 366898.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.081787 restraints weight = 181948.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.083556 restraints weight = 109661.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.084605 restraints weight = 75920.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.085232 restraints weight = 59618.085| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 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 = 0.4057 r_free = 0.4057 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: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23667 Z= 0.116 Angle : 0.570 6.942 32214 Z= 0.289 Chirality : 0.045 0.218 3538 Planarity : 0.005 0.050 4081 Dihedral : 8.819 159.991 3246 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 1.36 % Allowed : 19.67 % Favored : 78.98 % 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: -1.84 (0.16), residues: 2769 helix: 0.16 (0.25), residues: 453 sheet: -2.21 (0.18), residues: 741 loop : -1.07 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 231 TYR 0.027 0.001 TYR D 509 PHE 0.038 0.001 PHE B 751 TRP 0.034 0.001 TRP C 45 HIS 0.006 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (23667) covalent geometry : angle 0.57006 / 0.29 (32214) hydrogen bonds : bond 0.02979 / 2.25 ( 416) hydrogen bonds : angle 5.88267 / 4.24 ( 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 279 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.737 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: D 751 PHE cc_start: 0.7882 (m-10) cc_final: 0.7188 (m-80) REVERT: B 93 TYR cc_start: 0.8229 (m-80) cc_final: 0.7771 (m-80) REVERT: A 326 MET cc_start: 0.6877 (ppp) cc_final: 0.6363 (tmm) REVERT: A 332 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4834 (pp) REVERT: C 771 MET cc_start: 0.7251 (ppp) cc_final: 0.7018 (ptm) REVERT: C 786 LEU cc_start: 0.7673 (mt) cc_final: 0.7448 (mt) REVERT: C 833 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7843 (mt) outliers start: 35 outliers final: 31 residues processed: 270 average time/residue: 0.2468 time to fit residues: 102.4496 Evaluate side-chains 267 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 221 LEU 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 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 750 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 477 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 50 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 501 MET 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 Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 312 GLN ** 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.095972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.077574 restraints weight = 371461.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.080215 restraints weight = 187885.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.081782 restraints weight = 114364.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.082792 restraints weight = 81340.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.083372 restraints weight = 64546.406| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 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 = 0.4016 r_free = 0.4016 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 (3 function evaluations) r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23667 Z= 0.169 Angle : 0.603 10.956 32214 Z= 0.311 Chirality : 0.045 0.162 3538 Planarity : 0.005 0.075 4081 Dihedral : 8.935 160.575 3246 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 1.47 % Allowed : 19.71 % Favored : 78.82 % 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: -2.02 (0.16), residues: 2769 helix: 0.01 (0.25), residues: 453 sheet: -2.35 (0.18), residues: 758 loop : -1.15 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 778 TYR 0.031 0.002 TYR D 509 PHE 0.018 0.002 PHE C 710 TRP 0.032 0.002 TRP C 45 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (23667) covalent geometry : angle 0.60300 / 0.31 (32214) hydrogen bonds : bond 0.03238 / 2.33 ( 416) hydrogen bonds : angle 6.04872 / 4.37 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7396.72 seconds wall clock time: 126 minutes 50.70 seconds (7610.70 seconds total)