Starting phenix.real_space_refine on Wed Aug 27 02:46:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u61_41940/08_2025/8u61_41940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u61_41940/08_2025/8u61_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_41940/08_2025/8u61_41940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2025/8u61_41940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2025/8u61_41940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u61_41940/08_2025/8u61_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 11.74, per 1000 atoms: 0.26 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.76 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: 9.06 Time building geometry restraints manager: 4.86 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: 83712 1.89 - 3.78: 611 3.78 - 5.66: 33 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=" N PRO B 563 " pdb=" CA PRO B 563 " pdb=" C PRO B 563 " ideal model delta sigma weight residual 112.47 104.74 7.73 2.06e+00 2.36e-01 1.41e+01 angle pdb=" C SER C 270 " pdb=" CA SER C 270 " pdb=" CB SER C 270 " ideal model delta sigma weight residual 116.34 111.19 5.15 1.40e+00 5.10e-01 1.35e+01 angle pdb=" N VAL A 103 " pdb=" CA VAL A 103 " pdb=" C VAL A 103 " ideal model delta sigma weight residual 111.67 108.21 3.46 9.50e-01 1.11e+00 1.33e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 111.62 108.99 2.63 7.90e-01 1.60e+00 1.11e+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 - 0.029: 2042 0.029 - 0.057: 971 0.057 - 0.086: 196 0.086 - 0.115: 254 0.115 - 0.143: 75 Chirality restraints: 3538 Sorted by residual: chirality pdb=" CA ILE D 706 " pdb=" N ILE D 706 " pdb=" C ILE D 706 " pdb=" CB ILE D 706 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE B 706 " pdb=" N ILE B 706 " pdb=" C ILE B 706 " pdb=" CB ILE B 706 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-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: 8.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 40.810 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4368 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 0.031 23667 Z= 0.146 Angle : 0.572 9.441 32214 Z= 0.330 Chirality : 0.043 0.143 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 aren 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 covalent geometry : bond 0.00279 (23667) covalent geometry : angle 0.57171 (32214) hydrogen bonds : bond 0.19657 ( 416) hydrogen bonds : angle 8.37823 ( 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 : 1.089 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: 0.6957 (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: 0.4002 time to fit residues: 358.7488 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 : 0.883 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4500 r_free = 0.4500 target = 0.105166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.087164 restraints weight = 347368.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.090338 restraints weight = 169023.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.092339 restraints weight = 98832.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.093542 restraints weight = 66457.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.094254 restraints weight = 50570.065| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4258 r_free = 0.4258 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 = 0.4258 r_free = 0.4258 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23667 Z= 0.194 Angle : 0.649 7.077 32214 Z= 0.339 Chirality : 0.046 0.166 3538 Planarity : 0.005 0.062 4081 Dihedral : 8.650 161.161 3256 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.86 % Allowed : 17.34 % Favored : 80.80 % 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 aren not related in a simple way. whole: -1.57 (0.16), residues: 2769 helix: 0.24 (0.25), residues: 417 sheet: -1.79 (0.18), residues: 758 loop : -0.94 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 447 TYR 0.032 0.002 TYR D 287 PHE 0.019 0.002 PHE A 690 TRP 0.024 0.002 TRP C 228 HIS 0.009 0.001 HIS D 846 Details of bonding type rmsd covalent geometry : bond 0.00426 (23667) covalent geometry : angle 0.64934 (32214) hydrogen bonds : bond 0.04581 ( 416) hydrogen bonds : angle 6.73196 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 355 time to evaluate : 1.041 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: 0.8103 (mmmt) cc_final: 0.7855 (mmmt) REVERT: D 384 VAL cc_start: 0.6847 (t) cc_final: 0.6622 (t) REVERT: B 110 LEU cc_start: 0.4853 (tp) cc_final: 0.4468 (tp) REVERT: A 330 LEU cc_start: 0.8223 (mp) cc_final: 0.7949 (mm) REVERT: A 332 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4849 (pp) REVERT: A 335 PRO cc_start: 0.5467 (Cg_endo) cc_final: 0.5219 (Cg_exo) REVERT: C 381 LEU cc_start: 0.6652 (mt) cc_final: 0.6429 (mp) REVERT: C 833 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7726 (mt) outliers start: 48 outliers final: 29 residues processed: 392 average time/residue: 0.3740 time to fit residues: 220.4445 Evaluate side-chains 318 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 223 HIS Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 123 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 HIS ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 HIS B 212 ASN B 448 ASN B 697 HIS B 750 HIS B 760 HIS B 797 GLN A 683 GLN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 846 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 = 0.4426 r_free = 0.4426 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.082602 restraints weight = 359164.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.085604 restraints weight = 175919.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.087464 restraints weight = 104286.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.088620 restraints weight = 71651.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.089303 restraints weight = 55462.388| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 23667 Z= 0.226 Angle : 0.668 7.797 32214 Z= 0.354 Chirality : 0.046 0.184 3538 Planarity : 0.005 0.057 4081 Dihedral : 8.766 160.854 3247 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.40 % Allowed : 17.73 % Favored : 79.87 % 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 aren not related in a simple way. whole: -1.90 (0.16), residues: 2769 helix: -0.03 (0.24), residues: 415 sheet: -2.03 (0.18), residues: 762 loop : -1.14 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 472 TYR 0.027 0.002 TYR B 457 PHE 0.037 0.002 PHE C 710 TRP 0.020 0.002 TRP C 45 HIS 0.041 0.002 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00497 (23667) covalent geometry : angle 0.66809 (32214) hydrogen bonds : bond 0.04396 ( 416) hydrogen bonds : angle 6.61398 ( 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 347 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 1.087 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 141 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7970 (mmmt) REVERT: D 346 GLN cc_start: 0.7595 (mt0) cc_final: 0.7303 (tt0) REVERT: D 384 VAL cc_start: 0.6923 (t) cc_final: 0.6650 (t) REVERT: D 416 PHE cc_start: 0.7757 (m-80) cc_final: 0.7149 (m-80) REVERT: B 193 ASN cc_start: 0.5600 (p0) cc_final: 0.5028 (p0) REVERT: B 246 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6023 (mtmt) REVERT: A 332 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4855 (pp) REVERT: A 338 ASN cc_start: 0.6600 (t0) cc_final: 0.6076 (m110) REVERT: C 101 ASP cc_start: 0.3473 (OUTLIER) cc_final: 0.3147 (m-30) REVERT: C 265 LEU cc_start: 0.8471 (mp) cc_final: 0.8008 (tp) REVERT: C 358 HIS cc_start: 0.6851 (m-70) cc_final: 0.6458 (m-70) REVERT: C 833 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7914 (mt) outliers start: 62 outliers final: 40 residues processed: 328 average time/residue: 0.3482 time to fit residues: 175.3441 Evaluate side-chains 299 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 497 GLU 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 328 ILE 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 797 GLN Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 27 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 235 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 ASN B 312 GLN B 760 HIS ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.100709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.082601 restraints weight = 361104.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.085571 restraints weight = 171278.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.086784 restraints weight = 98308.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.086775 restraints weight = 92566.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.086971 restraints weight = 87582.909| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23667 Z= 0.159 Angle : 0.608 8.458 32214 Z= 0.314 Chirality : 0.045 0.182 3538 Planarity : 0.005 0.059 4081 Dihedral : 8.712 159.737 3247 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.98 % Allowed : 18.00 % Favored : 80.02 % 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 aren not related in a simple way. whole: -1.82 (0.16), residues: 2769 helix: 0.26 (0.25), residues: 417 sheet: -2.11 (0.18), residues: 775 loop : -1.07 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.016 0.002 TYR C 795 PHE 0.018 0.001 PHE C 710 TRP 0.025 0.001 TRP B 400 HIS 0.011 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00358 (23667) covalent geometry : angle 0.60769 (32214) hydrogen bonds : bond 0.03452 ( 416) hydrogen bonds : angle 6.24216 ( 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 319 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 1.179 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: D 346 GLN cc_start: 0.7615 (mt0) cc_final: 0.7262 (tt0) REVERT: D 374 ILE cc_start: 0.8845 (mt) cc_final: 0.8266 (mt) REVERT: D 384 VAL cc_start: 0.6769 (t) cc_final: 0.6528 (t) REVERT: D 416 PHE cc_start: 0.7803 (m-80) cc_final: 0.7278 (m-80) REVERT: D 805 LEU cc_start: 0.5822 (mm) cc_final: 0.5576 (mm) REVERT: A 326 MET cc_start: 0.6560 (ppp) cc_final: 0.6017 (tmm) REVERT: A 332 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.5048 (pp) REVERT: C 101 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3203 (m-30) REVERT: C 833 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8013 (mt) outliers start: 51 outliers final: 38 residues processed: 304 average time/residue: 0.3357 time to fit residues: 156.4551 Evaluate side-chains 291 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 ILE 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 760 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 538 GLU 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 101 ASP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 247 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 270 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 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: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.100557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.082044 restraints weight = 359094.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.084992 restraints weight = 176030.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.086885 restraints weight = 104356.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.088009 restraints weight = 71505.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.088666 restraints weight = 55339.086| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23667 Z= 0.124 Angle : 0.573 6.368 32214 Z= 0.294 Chirality : 0.045 0.155 3538 Planarity : 0.004 0.053 4081 Dihedral : 8.652 159.716 3247 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 18.08 % Favored : 80.18 % 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 aren not related in a simple way. whole: -1.72 (0.16), residues: 2769 helix: 0.35 (0.25), residues: 417 sheet: -2.05 (0.18), residues: 771 loop : -1.01 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.013 0.001 TYR C 307 PHE 0.020 0.001 PHE C 710 TRP 0.016 0.001 TRP C 45 HIS 0.012 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00293 (23667) covalent geometry : angle 0.57286 (32214) hydrogen bonds : bond 0.03231 ( 416) hydrogen bonds : angle 6.10248 ( 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 304 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 384 VAL cc_start: 0.6657 (t) cc_final: 0.6391 (t) REVERT: D 416 PHE cc_start: 0.7664 (m-80) cc_final: 0.7081 (m-80) REVERT: B 705 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7205 (p) REVERT: A 326 MET cc_start: 0.6391 (ppp) cc_final: 0.5921 (tmm) REVERT: A 332 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4878 (pp) REVERT: C 833 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7830 (mt) outliers start: 45 outliers final: 38 residues processed: 292 average time/residue: 0.3695 time to fit residues: 164.0958 Evaluate side-chains 290 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 760 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 538 GLU 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 129 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 GLN 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 373 CYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 186 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 67 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 ASN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS C 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.100283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.081558 restraints weight = 361485.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.084594 restraints weight = 174183.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.086474 restraints weight = 102356.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.087646 restraints weight = 69907.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.088306 restraints weight = 53864.391| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23667 Z= 0.123 Angle : 0.568 7.166 32214 Z= 0.290 Chirality : 0.044 0.176 3538 Planarity : 0.004 0.052 4081 Dihedral : 8.614 159.888 3246 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 1.86 % Allowed : 18.43 % Favored : 79.71 % 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 aren not related in a simple way. whole: -1.65 (0.16), residues: 2769 helix: 0.45 (0.25), residues: 417 sheet: -1.98 (0.18), residues: 763 loop : -0.99 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 490 TYR 0.012 0.001 TYR C 307 PHE 0.015 0.001 PHE C 710 TRP 0.030 0.001 TRP B 400 HIS 0.012 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00289 (23667) covalent geometry : angle 0.56847 (32214) hydrogen bonds : bond 0.03064 ( 416) hydrogen bonds : angle 6.01757 ( 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 305 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.891 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: D 384 VAL cc_start: 0.6581 (t) cc_final: 0.6324 (t) REVERT: D 416 PHE cc_start: 0.7795 (m-80) cc_final: 0.7163 (m-80) REVERT: D 751 PHE cc_start: 0.8136 (m-10) cc_final: 0.7372 (m-80) REVERT: D 805 LEU cc_start: 0.5610 (mm) cc_final: 0.5398 (mm) REVERT: B 705 SER cc_start: 0.7695 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 326 MET cc_start: 0.6631 (ppp) cc_final: 0.6109 (tmm) REVERT: A 332 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4989 (pp) REVERT: C 101 ASP cc_start: 0.3582 (OUTLIER) cc_final: 0.3137 (m-30) REVERT: C 833 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7800 (mt) outliers start: 48 outliers final: 36 residues processed: 290 average time/residue: 0.3355 time to fit residues: 150.3503 Evaluate side-chains 283 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 750 HIS 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 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 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 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 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 296 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 273 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 65 optimal weight: 0.4980 chunk 258 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 ASN B 312 GLN C 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.100739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.082048 restraints weight = 359035.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.085041 restraints weight = 174935.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.086961 restraints weight = 102997.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.088150 restraints weight = 69885.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.088846 restraints weight = 53865.023| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23667 Z= 0.102 Angle : 0.553 7.204 32214 Z= 0.279 Chirality : 0.045 0.325 3538 Planarity : 0.004 0.061 4081 Dihedral : 8.548 159.996 3246 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 1.32 % Allowed : 18.74 % Favored : 79.95 % 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 aren not related in a simple way. whole: -1.53 (0.16), residues: 2769 helix: 0.47 (0.25), residues: 428 sheet: -1.93 (0.18), residues: 763 loop : -0.88 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 490 TYR 0.012 0.001 TYR C 509 PHE 0.022 0.001 PHE D 213 TRP 0.024 0.001 TRP B 400 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00251 (23667) covalent geometry : angle 0.55275 (32214) hydrogen bonds : bond 0.02871 ( 416) hydrogen bonds : angle 5.80718 ( 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 298 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 384 VAL cc_start: 0.6527 (t) cc_final: 0.6272 (t) REVERT: D 416 PHE cc_start: 0.7651 (m-80) cc_final: 0.6996 (m-80) REVERT: B 93 TYR cc_start: 0.7952 (m-80) cc_final: 0.7286 (m-80) REVERT: A 326 MET cc_start: 0.6483 (ppp) cc_final: 0.6023 (tmm) REVERT: A 332 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4937 (pp) outliers start: 34 outliers final: 27 residues processed: 286 average time/residue: 0.3095 time to fit residues: 134.7556 Evaluate side-chains 276 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain 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 789 MET 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 477 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 210 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 193 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 ASN ** D 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 212 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.097511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.079258 restraints weight = 367401.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.081847 restraints weight = 188164.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.083464 restraints weight = 115045.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.084553 restraints weight = 81619.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.085183 restraints weight = 64397.609| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23667 Z= 0.187 Angle : 0.630 10.865 32214 Z= 0.328 Chirality : 0.045 0.205 3538 Planarity : 0.005 0.064 4081 Dihedral : 8.743 160.271 3246 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.31 % Rotamer: Outliers : 1.75 % Allowed : 18.46 % Favored : 79.79 % 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 aren not related in a simple way. whole: -1.82 (0.16), residues: 2769 helix: 0.14 (0.25), residues: 430 sheet: -2.06 (0.18), residues: 756 loop : -1.09 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 809 TYR 0.024 0.002 TYR D 77 PHE 0.022 0.002 PHE C 438 TRP 0.014 0.002 TRP D 202 HIS 0.011 0.002 HIS B 750 Details of bonding type rmsd covalent geometry : bond 0.00418 (23667) covalent geometry : angle 0.62955 (32214) hydrogen bonds : bond 0.03390 ( 416) hydrogen bonds : angle 6.15477 ( 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 295 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.819 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: D 384 VAL cc_start: 0.6539 (t) cc_final: 0.6253 (t) REVERT: D 507 TYR cc_start: 0.8031 (t80) cc_final: 0.7079 (t80) REVERT: B 711 MET cc_start: 0.8146 (mtt) cc_final: 0.7364 (mmm) REVERT: A 326 MET cc_start: 0.6843 (ppp) cc_final: 0.6368 (tmm) REVERT: A 332 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.5046 (pp) REVERT: A 357 ASN cc_start: 0.4261 (OUTLIER) cc_final: 0.3657 (t0) REVERT: C 101 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3257 (m-30) outliers start: 45 outliers final: 32 residues processed: 282 average time/residue: 0.2995 time to fit residues: 129.0687 Evaluate side-chains 268 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 557 THR 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 227 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.079661 restraints weight = 363009.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.082411 restraints weight = 179928.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.084175 restraints weight = 109012.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.085260 restraints weight = 76106.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085869 restraints weight = 59560.411| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23667 Z= 0.129 Angle : 0.586 7.626 32214 Z= 0.298 Chirality : 0.045 0.219 3538 Planarity : 0.005 0.053 4081 Dihedral : 8.713 158.946 3246 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 1.51 % Allowed : 18.97 % Favored : 79.52 % 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 aren not related in a simple way. whole: -1.77 (0.16), residues: 2769 helix: 0.29 (0.25), residues: 428 sheet: -2.05 (0.18), residues: 760 loop : -1.06 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 809 TYR 0.015 0.001 TYR C 119 PHE 0.020 0.001 PHE C 710 TRP 0.027 0.001 TRP C 45 HIS 0.009 0.001 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.00305 (23667) covalent geometry : angle 0.58576 (32214) hydrogen bonds : bond 0.03003 ( 416) hydrogen bonds : angle 5.91989 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.755 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: D 384 VAL cc_start: 0.6502 (t) cc_final: 0.6241 (t) REVERT: D 507 TYR cc_start: 0.7796 (t80) cc_final: 0.6914 (t80) REVERT: D 709 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4703 (pttp) REVERT: B 705 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7357 (p) REVERT: B 711 MET cc_start: 0.8054 (mtt) cc_final: 0.7335 (mmm) REVERT: A 326 MET cc_start: 0.6702 (ppp) cc_final: 0.6248 (tmm) REVERT: A 332 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5121 (pp) REVERT: C 101 ASP cc_start: 0.3567 (OUTLIER) cc_final: 0.3261 (m-30) outliers start: 39 outliers final: 28 residues processed: 270 average time/residue: 0.2727 time to fit residues: 113.0386 Evaluate side-chains 268 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 709 LYS Chi-restraints excluded: chain D residue 750 HIS 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 705 SER 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 528 LEU Chi-restraints excluded: chain A residue 690 PHE 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 227 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 115 optimal weight: 0.0570 chunk 158 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 ASN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080265 restraints weight = 363212.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.082836 restraints weight = 179957.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.083975 restraints weight = 106632.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.083904 restraints weight = 104769.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.084180 restraints weight = 93607.581| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23667 Z= 0.117 Angle : 0.571 7.695 32214 Z= 0.290 Chirality : 0.044 0.152 3538 Planarity : 0.005 0.056 4081 Dihedral : 8.674 159.158 3246 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 1.28 % Allowed : 19.36 % Favored : 79.36 % 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 aren not related in a simple way. whole: -1.69 (0.16), residues: 2769 helix: 0.39 (0.26), residues: 426 sheet: -2.05 (0.18), residues: 760 loop : -0.99 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 686 TYR 0.021 0.001 TYR D 77 PHE 0.018 0.001 PHE D 742 TRP 0.030 0.001 TRP C 45 HIS 0.009 0.001 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.00280 (23667) covalent geometry : angle 0.57105 (32214) hydrogen bonds : bond 0.02916 ( 416) hydrogen bonds : angle 5.82184 ( 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 281 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.750 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: 0.6294 (t) cc_final: 0.6040 (t) REVERT: D 709 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4703 (pttp) REVERT: B 705 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 711 MET cc_start: 0.8263 (mtt) cc_final: 0.7452 (mmm) REVERT: A 326 MET cc_start: 0.6743 (ppp) cc_final: 0.6256 (tmm) REVERT: A 332 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5171 (pp) REVERT: C 101 ASP cc_start: 0.3557 (OUTLIER) cc_final: 0.3204 (m-30) outliers start: 33 outliers final: 25 residues processed: 270 average time/residue: 0.2410 time to fit residues: 101.7706 Evaluate side-chains 268 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 709 LYS Chi-restraints excluded: chain D residue 750 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 TYR 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 705 SER 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 528 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 227 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 724 SER Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 0.6980 chunk 252 optimal weight: 0.0270 chunk 115 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 212 ASN ** A 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.097348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.078908 restraints weight = 366211.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.081572 restraints weight = 180895.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.083334 restraints weight = 109594.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.084384 restraints weight = 76392.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.085057 restraints weight = 59739.546| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23667 Z= 0.130 Angle : 0.576 8.048 32214 Z= 0.293 Chirality : 0.045 0.151 3538 Planarity : 0.005 0.057 4081 Dihedral : 8.660 159.546 3246 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 1.32 % Allowed : 19.39 % Favored : 79.29 % 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 aren not related in a simple way. whole: -1.71 (0.16), residues: 2769 helix: 0.35 (0.26), residues: 426 sheet: -2.14 (0.18), residues: 770 loop : -0.95 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 809 TYR 0.040 0.002 TYR D 509 PHE 0.042 0.001 PHE B 751 TRP 0.027 0.001 TRP C 45 HIS 0.007 0.001 HIS B 826 Details of bonding type rmsd covalent geometry : bond 0.00305 (23667) covalent geometry : angle 0.57607 (32214) hydrogen bonds : bond 0.02909 ( 416) hydrogen bonds : angle 5.80896 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7738.98 seconds wall clock time: 132 minutes 24.25 seconds (7944.25 seconds total)