Starting phenix.real_space_refine on Thu Mar 5 01:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxg_27055/03_2026/8cxg_27055.cif" } resolution = 3.2 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= 1.000 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11636 2.51 5 N 3149 2.21 5 O 3481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18381 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "l" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "B" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "1" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "2" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 846 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Time building chain proxies: 3.79, per 1000 atoms: 0.21 Number of scatterers: 18381 At special positions: 0 Unit cell: (107.06, 207.76, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3481 8.00 N 3149 7.00 C 11636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.08 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.72 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.51 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=1.75 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.08 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=1.38 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=1.18 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.79 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=1.24 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 629.2 milliseconds 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 31 sheets defined 20.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.576A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.634A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.696A pdb=" N HIS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.504A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.018A pdb=" N THR D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 40 through 53 removed outlier: 3.968A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'h' and resid 28 through 30 No H-bonds generated for 'chain 'h' and resid 28 through 30' Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.621A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.811A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.601A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.847A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.956A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 74 Proline residue: E 72 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.594A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.695A pdb=" N GLY C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 removed outlier: 3.889A pdb=" N THR F 9 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 removed outlier: 3.919A pdb=" N HIS F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 56 through 74 Proline residue: F 72 - end of helix Processing helix chain '1' and resid 28 through 30 No H-bonds generated for 'chain '1' and resid 28 through 30' Processing helix chain '1' and resid 87 through 91 Processing helix chain '2' and resid 79 through 83 removed outlier: 3.517A pdb=" N PHE 2 83 " --> pdb=" O PRO 2 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 110 through 112 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.608A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 126 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 129 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 210 through 214 removed outlier: 4.021A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.561A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 63 through 65 current: chain 'A' and resid 113 through 121 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 248 removed outlier: 3.751A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.724A pdb=" N THR A 315 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A 331 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 317 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 329 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.843A pdb=" N THR A 353 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 347 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A 345 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'h' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 11 through 12 current: chain 'h' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 58 through 60 current: chain 'h' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'l' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.660A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.587A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 51 current: chain 'B' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 129 current: chain 'B' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 169 current: chain 'B' and resid 210 through 214 removed outlier: 4.515A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 21 through 26 removed outlier: 4.638A pdb=" N LYS B 290 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC1, first strand: chain 'B' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 312 through 314 current: chain 'B' and resid 326 through 332 Processing sheet with id=AC2, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC3, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 50 current: chain 'C' and resid 112 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 129 current: chain 'C' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 164 through 169 current: chain 'C' and resid 210 through 214 removed outlier: 3.951A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 26 removed outlier: 4.605A pdb=" N LYS C 290 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 296 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER C 185 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AC7, first strand: chain 'C' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 312 through 314 current: chain 'C' and resid 326 through 332 Processing sheet with id=AC8, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.774A pdb=" N ILE C 389 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 396 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1' and resid 3 through 7 removed outlier: 3.577A pdb=" N LEU 1 20 " --> pdb=" O PHE 1 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 11 through 12 current: chain '1' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 58 through 60 current: chain '1' and resid 110 through 112 Processing sheet with id=AD3, first strand: chain '2' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain '2' and resid 10 through 13 removed outlier: 6.502A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1650 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: 3.11 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2975 1.29 - 1.43: 5117 1.43 - 1.57: 10529 1.57 - 1.72: 0 1.72 - 1.86: 179 Bond restraints: 18800 Sorted by residual: bond pdb=" CA CYS A 121 " pdb=" C CYS A 121 " ideal model delta sigma weight residual 1.522 1.408 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C VAL A 243 " pdb=" O VAL A 243 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.04e-02 9.25e+03 7.60e+01 bond pdb=" CA VAL A 243 " pdb=" CB VAL A 243 " ideal model delta sigma weight residual 1.541 1.459 0.082 1.28e-02 6.10e+03 4.15e+01 bond pdb=" CA PHE B 198 " pdb=" C PHE B 198 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.29e-02 6.01e+03 3.87e+01 bond pdb=" CA THR C 126 " pdb=" C THR C 126 " ideal model delta sigma weight residual 1.521 1.444 0.077 1.24e-02 6.50e+03 3.82e+01 ... (remaining 18795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 25046 3.05 - 6.10: 365 6.10 - 9.15: 62 9.15 - 12.20: 14 12.20 - 15.25: 4 Bond angle restraints: 25491 Sorted by residual: angle pdb=" N LEU C 242 " pdb=" CA LEU C 242 " pdb=" C LEU C 242 " ideal model delta sigma weight residual 113.17 100.84 12.33 1.26e+00 6.30e-01 9.58e+01 angle pdb=" N ASN B 237 " pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 111.36 121.20 -9.84 1.09e+00 8.42e-01 8.15e+01 angle pdb=" N PRO l 95 " pdb=" CA PRO l 95 " pdb=" C PRO l 95 " ideal model delta sigma weight residual 110.70 121.59 -10.89 1.22e+00 6.72e-01 7.97e+01 angle pdb=" N SER B 433 " pdb=" CA SER B 433 " pdb=" C SER B 433 " ideal model delta sigma weight residual 110.70 124.32 -13.62 1.55e+00 4.16e-01 7.72e+01 angle pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N LEU B 196 " ideal model delta sigma weight residual 117.04 125.73 -8.69 9.90e-01 1.02e+00 7.70e+01 ... (remaining 25486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10279 17.75 - 35.50: 620 35.50 - 53.25: 136 53.25 - 71.00: 38 71.00 - 88.75: 8 Dihedral angle restraints: 11081 sinusoidal: 4278 harmonic: 6803 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -174.75 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -156.44 70.44 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -149.85 63.85 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 11078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2748 0.123 - 0.246: 80 0.246 - 0.369: 10 0.369 - 0.492: 6 0.492 - 0.615: 4 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA LYS B 123 " pdb=" N LYS B 123 " pdb=" C LYS B 123 " pdb=" CB LYS B 123 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" CA MET C 349 " pdb=" N MET C 349 " pdb=" C MET C 349 " pdb=" CB MET C 349 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA LYS A 123 " pdb=" N LYS A 123 " pdb=" C LYS A 123 " pdb=" CB LYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2845 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 238 " -0.028 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN A 238 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN A 238 " -0.038 2.00e-02 2.50e+03 pdb=" N LYS A 239 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 121 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS B 121 " -0.078 2.00e-02 2.50e+03 pdb=" O CYS B 121 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 122 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 359 " 0.024 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE B 359 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 359 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 360 " 0.026 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 19 1.84 - 2.61: 385 2.61 - 3.37: 23225 3.37 - 4.14: 44280 4.14 - 4.90: 79722 Nonbonded interactions: 147631 Sorted by model distance: nonbonded pdb=" NH2 ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.081 3.120 nonbonded pdb=" CZ ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.192 3.270 nonbonded pdb=" CG PRO C 224 " pdb=" CD1 LEU C 242 " model vdw 1.266 3.860 nonbonded pdb=" O GLY B 104 " pdb=" CE2 PHE 2 32 " model vdw 1.284 3.340 nonbonded pdb=" O ASN B 238 " pdb=" OE1 GLU B 240 " model vdw 1.324 3.040 ... (remaining 147626 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 '1' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '2' selection = (chain 'L' and resid 1 through 108) selection = (chain 'l' and resid 1 through 108) } ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 150 or resid 160 through 501)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.015 0.846 18826 Z= 0.830 Angle : 1.133 54.670 25535 Z= 0.660 Chirality : 0.061 0.615 2848 Planarity : 0.006 0.088 3232 Dihedral : 12.574 85.278 6687 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.77 % Favored : 90.81 % Rotamer: Outliers : 2.73 % Allowed : 8.04 % Favored : 89.23 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.16), residues: 2371 helix: -0.76 (0.23), residues: 421 sheet: -0.34 (0.18), residues: 767 loop : -2.50 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 193 TYR 0.024 0.002 TYR E 25 PHE 0.015 0.002 PHE F 42 TRP 0.022 0.002 TRP C 101 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00828 (18800) covalent geometry : angle 0.96072 (25491) SS BOND : bond 0.35311 ( 22) SS BOND : angle 14.48709 ( 44) hydrogen bonds : bond 0.14277 ( 630) hydrogen bonds : angle 6.90880 ( 1650) Misc. bond : bond 0.23324 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 410 time to evaluate : 0.678 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: H 34 MET cc_start: 0.9321 (mmm) cc_final: 0.8978 (mmm) REVERT: H 57 SER cc_start: 0.7649 (t) cc_final: 0.7391 (p) REVERT: H 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8749 (m) REVERT: A 491 LEU cc_start: 0.5658 (mt) cc_final: 0.5279 (mt) REVERT: B 466 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7760 (tt) REVERT: C 349 MET cc_start: 0.6015 (mmm) cc_final: 0.4933 (ptp) REVERT: C 460 MET cc_start: 0.7468 (ptp) cc_final: 0.7186 (ptp) REVERT: 1 109 MET cc_start: 0.0576 (mtp) cc_final: -0.2072 (mtm) outliers start: 54 outliers final: 19 residues processed: 456 average time/residue: 0.1155 time to fit residues: 83.1111 Evaluate side-chains 332 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain 2 residue 94 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 148 HIS A 163 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 478 ASN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 17 GLN h 39 GLN l 42 GLN l 90 GLN B 85 GLN B 103 ASN B 148 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS E 39 ASN C 103 ASN C 134 ASN C 163 ASN C 350 GLN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN C 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN 2 42 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116814 restraints weight = 36735.361| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.18 r_work: 0.3071 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 18826 Z= 0.214 Angle : 0.751 19.146 25535 Z= 0.389 Chirality : 0.047 0.298 2848 Planarity : 0.006 0.135 3232 Dihedral : 6.540 57.743 2616 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.19 % Favored : 90.76 % Rotamer: Outliers : 4.25 % Allowed : 13.85 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.17), residues: 2371 helix: -0.10 (0.24), residues: 439 sheet: -0.11 (0.18), residues: 833 loop : -2.11 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.015 0.001 TYR A 61 PHE 0.016 0.002 PHE F 42 TRP 0.026 0.002 TRP B 400 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00489 (18800) covalent geometry : angle 0.75034 (25491) SS BOND : bond 0.00634 ( 22) SS BOND : angle 1.23422 ( 44) hydrogen bonds : bond 0.04891 ( 630) hydrogen bonds : angle 5.65865 ( 1650) Misc. bond : bond 0.00284 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 331 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8616 (mmm) cc_final: 0.8178 (mmm) REVERT: H 57 SER cc_start: 0.4676 (t) cc_final: 0.4398 (p) REVERT: H 97 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7400 (m) REVERT: H 116 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 68 MET cc_start: 0.9302 (mpp) cc_final: 0.9003 (mpp) REVERT: A 254 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8617 (p) REVERT: A 377 GLU cc_start: 0.8815 (pt0) cc_final: 0.8512 (pt0) REVERT: A 412 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8810 (mm-30) REVERT: A 498 LEU cc_start: 0.8501 (mp) cc_final: 0.8255 (mp) REVERT: h 93 VAL cc_start: 0.8199 (t) cc_final: 0.7976 (p) REVERT: B 36 GLN cc_start: 0.8959 (tp40) cc_final: 0.8748 (tp40) REVERT: B 68 MET cc_start: 0.8963 (mpp) cc_final: 0.8713 (mpp) REVERT: B 191 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 197 ASP cc_start: 0.8471 (t0) cc_final: 0.8231 (t0) REVERT: B 308 CYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8709 (m) REVERT: B 412 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8597 (mm-30) REVERT: E 14 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.8989 (p) REVERT: E 33 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 197 ASP cc_start: 0.8902 (t0) cc_final: 0.8391 (t0) REVERT: C 295 MET cc_start: 0.9441 (ptm) cc_final: 0.9222 (ptp) REVERT: C 349 MET cc_start: 0.7457 (mmm) cc_final: 0.5986 (ptp) REVERT: C 478 ASN cc_start: 0.8322 (m-40) cc_final: 0.8070 (m110) REVERT: F 33 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8814 (tm-30) REVERT: 1 109 MET cc_start: -0.2333 (mtp) cc_final: -0.3379 (mtm) outliers start: 84 outliers final: 41 residues processed: 387 average time/residue: 0.1060 time to fit residues: 66.9512 Evaluate side-chains 350 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 165 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 227 optimal weight: 40.0000 chunk 97 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 40.0000 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 40.0000 chunk 110 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN C 134 ASN C 148 HIS ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119905 restraints weight = 37042.355| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.27 r_work: 0.3102 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18826 Z= 0.145 Angle : 0.652 10.781 25535 Z= 0.342 Chirality : 0.044 0.254 2848 Planarity : 0.005 0.109 3232 Dihedral : 5.804 57.345 2596 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.81 % Favored : 91.14 % Rotamer: Outliers : 4.10 % Allowed : 16.08 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.17), residues: 2371 helix: 0.47 (0.26), residues: 422 sheet: 0.25 (0.19), residues: 813 loop : -1.91 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 31 TYR 0.015 0.001 TYR A 61 PHE 0.014 0.001 PHE F 42 TRP 0.018 0.001 TRP B 400 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00326 (18800) covalent geometry : angle 0.65154 (25491) SS BOND : bond 0.00370 ( 22) SS BOND : angle 0.93364 ( 44) hydrogen bonds : bond 0.04358 ( 630) hydrogen bonds : angle 5.41304 ( 1650) Misc. bond : bond 0.00182 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 330 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8719 (mmm) cc_final: 0.8342 (mmm) REVERT: H 57 SER cc_start: 0.3790 (t) cc_final: 0.3512 (p) REVERT: H 97 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7591 (m) REVERT: L 94 TRP cc_start: 0.6672 (OUTLIER) cc_final: 0.4864 (t60) REVERT: A 254 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8623 (p) REVERT: A 320 GLU cc_start: 0.8701 (tt0) cc_final: 0.8437 (tt0) REVERT: A 350 GLN cc_start: 0.7944 (mp10) cc_final: 0.7704 (mp10) REVERT: A 412 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8783 (mm-30) REVERT: A 472 LEU cc_start: 0.8719 (mt) cc_final: 0.8461 (mt) REVERT: D 25 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.5429 (p90) REVERT: D 33 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8021 (tm-30) REVERT: h 60 TYR cc_start: 0.8356 (m-80) cc_final: 0.8055 (m-80) REVERT: h 93 VAL cc_start: 0.8168 (t) cc_final: 0.7951 (p) REVERT: l 91 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8115 (mmt90) REVERT: B 36 GLN cc_start: 0.8934 (tp40) cc_final: 0.8654 (tp40) REVERT: B 68 MET cc_start: 0.8916 (mpp) cc_final: 0.8657 (mpp) REVERT: B 107 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9253 (mt) REVERT: B 197 ASP cc_start: 0.8372 (t0) cc_final: 0.7955 (p0) REVERT: B 308 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 377 GLU cc_start: 0.9072 (pt0) cc_final: 0.8834 (tt0) REVERT: B 412 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8575 (mm-30) REVERT: E 14 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9147 (p) REVERT: E 33 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 197 ASP cc_start: 0.8938 (t0) cc_final: 0.8473 (t0) REVERT: C 307 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9286 (pp) REVERT: C 349 MET cc_start: 0.7696 (mmm) cc_final: 0.6046 (ptp) REVERT: C 474 TRP cc_start: 0.8516 (t-100) cc_final: 0.8252 (t-100) REVERT: C 478 ASN cc_start: 0.8524 (m-40) cc_final: 0.7990 (m-40) REVERT: F 14 THR cc_start: 0.9432 (t) cc_final: 0.9176 (m) REVERT: F 33 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8798 (tm-30) REVERT: 1 109 MET cc_start: -0.2276 (mtp) cc_final: -0.3387 (mtm) outliers start: 81 outliers final: 44 residues processed: 383 average time/residue: 0.1048 time to fit residues: 65.5537 Evaluate side-chains 367 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 178 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 32 optimal weight: 0.0670 chunk 214 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.0020 chunk 122 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 173 optimal weight: 1.9990 overall best weight: 2.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 HIS l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121477 restraints weight = 37121.870| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.26 r_work: 0.3124 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18826 Z= 0.129 Angle : 0.616 10.112 25535 Z= 0.323 Chirality : 0.043 0.254 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.430 53.802 2592 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.15 % Favored : 90.81 % Rotamer: Outliers : 4.10 % Allowed : 17.34 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2371 helix: 0.64 (0.26), residues: 422 sheet: 0.43 (0.19), residues: 801 loop : -1.77 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 31 TYR 0.011 0.001 TYR H 105 PHE 0.014 0.001 PHE F 42 TRP 0.015 0.001 TRP B 400 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00289 (18800) covalent geometry : angle 0.61538 (25491) SS BOND : bond 0.00309 ( 22) SS BOND : angle 0.76316 ( 44) hydrogen bonds : bond 0.04077 ( 630) hydrogen bonds : angle 5.25215 ( 1650) Misc. bond : bond 0.00158 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.3276 (t) cc_final: 0.2941 (p) REVERT: H 95 TYR cc_start: 0.7330 (m-80) cc_final: 0.7088 (m-80) REVERT: H 107 TYR cc_start: 0.9266 (p90) cc_final: 0.8838 (p90) REVERT: H 116 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7447 (p) REVERT: L 94 TRP cc_start: 0.6246 (OUTLIER) cc_final: 0.4519 (t60) REVERT: A 394 LYS cc_start: 0.9455 (mmmm) cc_final: 0.9208 (mmmm) REVERT: A 412 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8796 (mm-30) REVERT: D 25 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.5380 (p90) REVERT: h 60 TYR cc_start: 0.8432 (m-80) cc_final: 0.8104 (m-80) REVERT: h 80 TYR cc_start: 0.7856 (m-80) cc_final: 0.7474 (m-80) REVERT: h 93 VAL cc_start: 0.8114 (t) cc_final: 0.7896 (p) REVERT: l 91 ARG cc_start: 0.8429 (mmt90) cc_final: 0.7978 (mtt180) REVERT: B 15 MET cc_start: 0.7300 (tmm) cc_final: 0.7079 (tmm) REVERT: B 36 GLN cc_start: 0.8938 (tp40) cc_final: 0.8621 (tp40) REVERT: B 68 MET cc_start: 0.8919 (mpp) cc_final: 0.8668 (mpp) REVERT: B 140 MET cc_start: 0.8934 (mmm) cc_final: 0.8609 (mmm) REVERT: B 191 GLU cc_start: 0.8148 (tp30) cc_final: 0.7694 (tm-30) REVERT: B 197 ASP cc_start: 0.8456 (t0) cc_final: 0.7939 (p0) REVERT: B 308 CYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8561 (m) REVERT: B 377 GLU cc_start: 0.8997 (pt0) cc_final: 0.8661 (tt0) REVERT: B 412 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8570 (mm-30) REVERT: E 14 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9137 (p) REVERT: E 33 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 197 ASP cc_start: 0.8980 (t0) cc_final: 0.8563 (t0) REVERT: C 307 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9266 (pp) REVERT: C 349 MET cc_start: 0.7847 (mmm) cc_final: 0.6418 (ptp) REVERT: C 474 TRP cc_start: 0.8515 (t-100) cc_final: 0.8228 (t-100) REVERT: C 475 LEU cc_start: 0.8868 (tp) cc_final: 0.8643 (tt) REVERT: C 478 ASN cc_start: 0.8495 (m-40) cc_final: 0.7994 (m-40) REVERT: F 21 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: F 33 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8751 (tm-30) REVERT: 1 109 MET cc_start: -0.2359 (mtp) cc_final: -0.3855 (mtm) outliers start: 81 outliers final: 50 residues processed: 384 average time/residue: 0.1135 time to fit residues: 70.7270 Evaluate side-chains 372 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 45 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 226 optimal weight: 0.0170 chunk 210 optimal weight: 5.9990 overall best weight: 3.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 144 HIS B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120057 restraints weight = 36901.980| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.16 r_work: 0.3090 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18826 Z= 0.147 Angle : 0.620 10.463 25535 Z= 0.324 Chirality : 0.043 0.266 2848 Planarity : 0.005 0.091 3232 Dihedral : 5.284 52.802 2589 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.11 % Favored : 90.85 % Rotamer: Outliers : 4.65 % Allowed : 17.39 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2371 helix: 0.73 (0.26), residues: 423 sheet: 0.58 (0.19), residues: 792 loop : -1.74 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.023 0.001 TYR H 105 PHE 0.013 0.001 PHE F 42 TRP 0.014 0.001 TRP B 400 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00335 (18800) covalent geometry : angle 0.61941 (25491) SS BOND : bond 0.00356 ( 22) SS BOND : angle 0.85351 ( 44) hydrogen bonds : bond 0.04076 ( 630) hydrogen bonds : angle 5.20310 ( 1650) Misc. bond : bond 0.00167 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 326 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8629 (mmm) cc_final: 0.8389 (mmm) REVERT: H 57 SER cc_start: 0.3420 (t) cc_final: 0.3166 (p) REVERT: H 95 TYR cc_start: 0.7376 (m-80) cc_final: 0.7149 (m-80) REVERT: H 116 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7521 (p) REVERT: L 94 TRP cc_start: 0.6130 (OUTLIER) cc_final: 0.4224 (t60) REVERT: D 25 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.5334 (p90) REVERT: h 93 VAL cc_start: 0.8129 (t) cc_final: 0.7906 (p) REVERT: h 111 VAL cc_start: 0.8522 (t) cc_final: 0.8164 (m) REVERT: l 91 ARG cc_start: 0.8483 (mmt90) cc_final: 0.7971 (mtt180) REVERT: B 36 GLN cc_start: 0.8995 (tp40) cc_final: 0.8676 (tp40) REVERT: B 68 MET cc_start: 0.8881 (mpp) cc_final: 0.8612 (mpp) REVERT: B 140 MET cc_start: 0.8963 (mmm) cc_final: 0.8603 (mmm) REVERT: B 191 GLU cc_start: 0.7932 (tp30) cc_final: 0.7674 (pp20) REVERT: B 197 ASP cc_start: 0.8424 (t0) cc_final: 0.7842 (p0) REVERT: B 308 CYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 377 GLU cc_start: 0.9012 (pt0) cc_final: 0.8661 (tt0) REVERT: B 412 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8583 (mm-30) REVERT: B 473 MET cc_start: 0.8123 (tpp) cc_final: 0.7761 (mmt) REVERT: E 14 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9127 (p) REVERT: E 33 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8300 (tm-30) REVERT: C 89 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8904 (mt0) REVERT: C 197 ASP cc_start: 0.9001 (t0) cc_final: 0.8484 (t0) REVERT: C 202 TYR cc_start: 0.9233 (m-80) cc_final: 0.8981 (m-10) REVERT: C 307 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9292 (pp) REVERT: C 349 MET cc_start: 0.7900 (mmm) cc_final: 0.6425 (ptp) REVERT: C 473 MET cc_start: 0.8705 (mmm) cc_final: 0.8377 (mmt) REVERT: C 474 TRP cc_start: 0.8495 (t-100) cc_final: 0.8251 (t-100) REVERT: C 475 LEU cc_start: 0.8873 (tp) cc_final: 0.8638 (tt) REVERT: C 478 ASN cc_start: 0.8489 (m-40) cc_final: 0.7916 (m-40) REVERT: F 21 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: F 33 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8750 (tm-30) REVERT: 1 109 MET cc_start: -0.2331 (mtp) cc_final: -0.3850 (mtm) outliers start: 92 outliers final: 58 residues processed: 388 average time/residue: 0.1084 time to fit residues: 68.2703 Evaluate side-chains 382 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 316 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 83 MET Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 224 optimal weight: 50.0000 chunk 165 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115983 restraints weight = 37359.624| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.09 r_work: 0.3016 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 18826 Z= 0.286 Angle : 0.717 13.059 25535 Z= 0.374 Chirality : 0.046 0.280 2848 Planarity : 0.005 0.092 3232 Dihedral : 5.588 57.959 2589 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.00 % Rotamer: Outliers : 5.01 % Allowed : 18.35 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2371 helix: 0.64 (0.26), residues: 423 sheet: 0.50 (0.19), residues: 814 loop : -1.71 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.027 0.002 TYR H 105 PHE 0.017 0.002 PHE A 431 TRP 0.018 0.002 TRP C 101 HIS 0.022 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00651 (18800) covalent geometry : angle 0.71608 (25491) SS BOND : bond 0.00568 ( 22) SS BOND : angle 1.10485 ( 44) hydrogen bonds : bond 0.04734 ( 630) hydrogen bonds : angle 5.33992 ( 1650) Misc. bond : bond 0.00258 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 299 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.4576 (t) cc_final: 0.4323 (p) REVERT: H 107 TYR cc_start: 0.9226 (p90) cc_final: 0.9022 (p90) REVERT: H 116 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7406 (p) REVERT: L 94 TRP cc_start: 0.6486 (OUTLIER) cc_final: 0.4492 (t60) REVERT: A 285 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8796 (t) REVERT: A 350 GLN cc_start: 0.8257 (mp10) cc_final: 0.7899 (mp10) REVERT: D 25 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.5365 (p90) REVERT: D 74 TYR cc_start: 0.4677 (OUTLIER) cc_final: 0.2953 (m-80) REVERT: h 60 TYR cc_start: 0.8338 (m-80) cc_final: 0.8112 (m-80) REVERT: h 93 VAL cc_start: 0.8062 (t) cc_final: 0.7819 (p) REVERT: h 111 VAL cc_start: 0.8446 (t) cc_final: 0.8095 (m) REVERT: l 91 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8024 (mtt180) REVERT: B 36 GLN cc_start: 0.9143 (tp40) cc_final: 0.8843 (tp40) REVERT: B 140 MET cc_start: 0.8986 (mmm) cc_final: 0.8604 (mmm) REVERT: B 197 ASP cc_start: 0.8497 (t0) cc_final: 0.7898 (p0) REVERT: B 308 CYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8663 (m) REVERT: B 412 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8628 (mm-30) REVERT: B 433 SER cc_start: 0.9108 (t) cc_final: 0.8713 (p) REVERT: B 438 LEU cc_start: 0.8567 (mt) cc_final: 0.8214 (tp) REVERT: E 14 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9169 (p) REVERT: E 33 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 89 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9039 (tt0) REVERT: C 197 ASP cc_start: 0.9042 (t0) cc_final: 0.8584 (t0) REVERT: C 286 SER cc_start: 0.9268 (p) cc_final: 0.9030 (p) REVERT: C 307 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9385 (pp) REVERT: C 349 MET cc_start: 0.8086 (mmm) cc_final: 0.6558 (ptp) REVERT: C 379 ASP cc_start: 0.9004 (t0) cc_final: 0.8767 (t0) REVERT: C 478 ASN cc_start: 0.8410 (m-40) cc_final: 0.8117 (m-40) REVERT: F 33 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8880 (tm-30) REVERT: 1 109 MET cc_start: -0.2294 (mtp) cc_final: -0.3756 (mtm) outliers start: 99 outliers final: 65 residues processed: 364 average time/residue: 0.1076 time to fit residues: 63.8481 Evaluate side-chains 368 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 20 optimal weight: 40.0000 chunk 143 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 221 optimal weight: 30.0000 chunk 218 optimal weight: 9.9990 chunk 17 optimal weight: 40.0000 chunk 200 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 HIS l 90 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.116913 restraints weight = 37297.206| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.20 r_work: 0.3044 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18826 Z= 0.181 Angle : 0.660 12.076 25535 Z= 0.344 Chirality : 0.044 0.223 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.488 56.047 2589 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.66 % Favored : 90.30 % Rotamer: Outliers : 4.55 % Allowed : 19.26 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2371 helix: 0.66 (0.26), residues: 423 sheet: 0.63 (0.19), residues: 800 loop : -1.71 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.018 0.001 TYR H 105 PHE 0.013 0.001 PHE F 42 TRP 0.013 0.001 TRP B 236 HIS 0.011 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00414 (18800) covalent geometry : angle 0.65994 (25491) SS BOND : bond 0.00421 ( 22) SS BOND : angle 0.91722 ( 44) hydrogen bonds : bond 0.04380 ( 630) hydrogen bonds : angle 5.32974 ( 1650) Misc. bond : bond 0.00212 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 299 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7405 (p) REVERT: L 94 TRP cc_start: 0.6377 (OUTLIER) cc_final: 0.4327 (t60) REVERT: A 295 MET cc_start: 0.9398 (ptp) cc_final: 0.9110 (pmm) REVERT: A 350 GLN cc_start: 0.8296 (mp10) cc_final: 0.7900 (mp10) REVERT: D 25 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.5271 (p90) REVERT: h 60 TYR cc_start: 0.8259 (m-80) cc_final: 0.7997 (m-80) REVERT: h 93 VAL cc_start: 0.8039 (t) cc_final: 0.7809 (p) REVERT: h 111 VAL cc_start: 0.8405 (t) cc_final: 0.8060 (m) REVERT: l 91 ARG cc_start: 0.8405 (mmt90) cc_final: 0.7901 (mtt180) REVERT: B 36 GLN cc_start: 0.9147 (tp40) cc_final: 0.8874 (tp40) REVERT: B 140 MET cc_start: 0.8951 (mmm) cc_final: 0.8533 (mmm) REVERT: B 197 ASP cc_start: 0.8517 (t0) cc_final: 0.7898 (p0) REVERT: B 240 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 277 MET cc_start: 0.8558 (ttt) cc_final: 0.8318 (tpp) REVERT: B 308 CYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 412 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8604 (mm-30) REVERT: B 433 SER cc_start: 0.9097 (t) cc_final: 0.8760 (p) REVERT: E 14 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9171 (p) REVERT: E 33 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 89 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9049 (mt0) REVERT: C 197 ASP cc_start: 0.9101 (t0) cc_final: 0.8631 (t0) REVERT: C 286 SER cc_start: 0.9249 (p) cc_final: 0.9017 (p) REVERT: C 307 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9341 (pp) REVERT: C 349 MET cc_start: 0.8305 (mmm) cc_final: 0.6534 (ptp) REVERT: C 379 ASP cc_start: 0.9007 (t0) cc_final: 0.8724 (t0) REVERT: C 473 MET cc_start: 0.8813 (mmm) cc_final: 0.8592 (mmt) REVERT: C 478 ASN cc_start: 0.8373 (m-40) cc_final: 0.8100 (m-40) REVERT: F 21 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: F 33 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8852 (tm-30) REVERT: 1 109 MET cc_start: -0.2421 (mtp) cc_final: -0.3702 (mtm) outliers start: 90 outliers final: 61 residues processed: 358 average time/residue: 0.1120 time to fit residues: 65.1097 Evaluate side-chains 366 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 188 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.116321 restraints weight = 36888.497| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.13 r_work: 0.3034 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18826 Z= 0.191 Angle : 0.670 12.073 25535 Z= 0.347 Chirality : 0.045 0.241 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.468 55.606 2589 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.00 % Rotamer: Outliers : 4.40 % Allowed : 19.62 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2371 helix: 0.65 (0.26), residues: 423 sheet: 0.71 (0.19), residues: 790 loop : -1.71 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 31 TYR 0.025 0.001 TYR H 107 PHE 0.013 0.001 PHE A 431 TRP 0.014 0.001 TRP B 400 HIS 0.007 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00435 (18800) covalent geometry : angle 0.66942 (25491) SS BOND : bond 0.00441 ( 22) SS BOND : angle 0.92514 ( 44) hydrogen bonds : bond 0.04346 ( 630) hydrogen bonds : angle 5.32518 ( 1650) Misc. bond : bond 0.00275 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.4441 (t) cc_final: 0.4206 (p) REVERT: H 116 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7224 (p) REVERT: L 94 TRP cc_start: 0.6399 (OUTLIER) cc_final: 0.4324 (t60) REVERT: A 350 GLN cc_start: 0.8370 (mp10) cc_final: 0.7955 (mp10) REVERT: A 394 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9100 (mmmm) REVERT: A 496 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7565 (tp) REVERT: D 25 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.5296 (p90) REVERT: D 74 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.2952 (m-80) REVERT: h 93 VAL cc_start: 0.8096 (t) cc_final: 0.7866 (p) REVERT: l 91 ARG cc_start: 0.8462 (mmt90) cc_final: 0.7912 (mtt180) REVERT: B 36 GLN cc_start: 0.9160 (tp40) cc_final: 0.8898 (tp40) REVERT: B 140 MET cc_start: 0.8941 (mmm) cc_final: 0.8540 (mmm) REVERT: B 197 ASP cc_start: 0.8529 (t0) cc_final: 0.7886 (p0) REVERT: B 240 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 277 MET cc_start: 0.8575 (ttt) cc_final: 0.8356 (tpp) REVERT: B 308 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8695 (m) REVERT: B 412 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8607 (mm-30) REVERT: B 433 SER cc_start: 0.9148 (t) cc_final: 0.8844 (p) REVERT: B 438 LEU cc_start: 0.8533 (mt) cc_final: 0.8228 (tp) REVERT: E 14 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9181 (p) REVERT: E 33 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 89 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.9029 (mt0) REVERT: C 151 MET cc_start: 0.7808 (mmt) cc_final: 0.7415 (mmm) REVERT: C 197 ASP cc_start: 0.9056 (t0) cc_final: 0.8673 (t0) REVERT: C 286 SER cc_start: 0.9230 (p) cc_final: 0.8995 (p) REVERT: C 295 MET cc_start: 0.9398 (ptp) cc_final: 0.9034 (ptp) REVERT: C 307 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9368 (pp) REVERT: C 349 MET cc_start: 0.8338 (mmm) cc_final: 0.6592 (ptp) REVERT: C 379 ASP cc_start: 0.9042 (t0) cc_final: 0.8725 (t0) REVERT: C 478 ASN cc_start: 0.8401 (m-40) cc_final: 0.8096 (m-40) REVERT: F 21 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: F 33 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8863 (tm-30) REVERT: 1 83 MET cc_start: 0.6455 (ptm) cc_final: 0.6240 (ptm) REVERT: 1 109 MET cc_start: -0.2034 (mtp) cc_final: -0.3501 (mtm) outliers start: 87 outliers final: 68 residues processed: 357 average time/residue: 0.1051 time to fit residues: 61.9938 Evaluate side-chains 376 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 179 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 219 optimal weight: 50.0000 chunk 122 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115203 restraints weight = 36746.309| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.07 r_work: 0.2991 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18826 Z= 0.237 Angle : 0.696 13.040 25535 Z= 0.361 Chirality : 0.046 0.239 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.556 56.978 2589 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.00 % Rotamer: Outliers : 4.55 % Allowed : 19.97 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2371 helix: 0.66 (0.26), residues: 423 sheet: 0.65 (0.19), residues: 801 loop : -1.69 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG l 91 TYR 0.024 0.001 TYR H 107 PHE 0.014 0.001 PHE A 431 TRP 0.014 0.001 TRP C 101 HIS 0.009 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00543 (18800) covalent geometry : angle 0.69547 (25491) SS BOND : bond 0.00505 ( 22) SS BOND : angle 1.00752 ( 44) hydrogen bonds : bond 0.04554 ( 630) hydrogen bonds : angle 5.35886 ( 1650) Misc. bond : bond 0.00263 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 295 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.4578 (t) cc_final: 0.4284 (p) REVERT: H 116 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7139 (p) REVERT: L 94 TRP cc_start: 0.6447 (OUTLIER) cc_final: 0.4311 (t60) REVERT: A 350 GLN cc_start: 0.8362 (mp10) cc_final: 0.7991 (mp10) REVERT: A 394 LYS cc_start: 0.9433 (mmmm) cc_final: 0.9080 (mmmm) REVERT: A 496 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7656 (tp) REVERT: D 25 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.5397 (p90) REVERT: D 74 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.3000 (m-80) REVERT: h 93 VAL cc_start: 0.8081 (t) cc_final: 0.7848 (p) REVERT: l 91 ARG cc_start: 0.8510 (mmt90) cc_final: 0.8042 (mtt-85) REVERT: B 36 GLN cc_start: 0.9203 (tp40) cc_final: 0.8937 (tp40) REVERT: B 140 MET cc_start: 0.8942 (mmm) cc_final: 0.8536 (mmm) REVERT: B 197 ASP cc_start: 0.8552 (t0) cc_final: 0.7905 (p0) REVERT: B 240 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: B 251 LYS cc_start: 0.8668 (ptmm) cc_final: 0.8184 (pttp) REVERT: B 277 MET cc_start: 0.8549 (ttt) cc_final: 0.8342 (tpp) REVERT: B 308 CYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 412 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8626 (mm-30) REVERT: B 433 SER cc_start: 0.9265 (t) cc_final: 0.9014 (p) REVERT: B 438 LEU cc_start: 0.8635 (mt) cc_final: 0.8409 (tt) REVERT: E 14 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9238 (p) REVERT: E 33 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 89 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9078 (mt0) REVERT: C 151 MET cc_start: 0.7767 (mmt) cc_final: 0.7458 (mmm) REVERT: C 197 ASP cc_start: 0.9087 (t0) cc_final: 0.8758 (t0) REVERT: C 286 SER cc_start: 0.9236 (p) cc_final: 0.9001 (p) REVERT: C 295 MET cc_start: 0.9381 (ptp) cc_final: 0.9078 (ptp) REVERT: C 307 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9394 (pp) REVERT: C 349 MET cc_start: 0.8328 (mmm) cc_final: 0.6590 (ptp) REVERT: C 379 ASP cc_start: 0.9032 (t0) cc_final: 0.8708 (t0) REVERT: C 478 ASN cc_start: 0.8395 (m-40) cc_final: 0.8116 (m-40) REVERT: F 21 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: F 33 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8866 (tm-30) REVERT: 1 83 MET cc_start: 0.6497 (ptm) cc_final: 0.6296 (ptm) REVERT: 1 109 MET cc_start: -0.2585 (mtp) cc_final: -0.4239 (mpp) outliers start: 90 outliers final: 70 residues processed: 348 average time/residue: 0.1096 time to fit residues: 62.6662 Evaluate side-chains 376 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 113 optimal weight: 3.9990 chunk 229 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 183 optimal weight: 20.0000 chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 91 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115662 restraints weight = 36862.841| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.10 r_work: 0.3015 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18826 Z= 0.204 Angle : 0.680 11.640 25535 Z= 0.352 Chirality : 0.045 0.208 2848 Planarity : 0.005 0.095 3232 Dihedral : 5.536 56.290 2589 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.00 % Favored : 89.96 % Rotamer: Outliers : 4.40 % Allowed : 20.02 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2371 helix: 0.67 (0.26), residues: 423 sheet: 0.72 (0.20), residues: 792 loop : -1.67 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 31 TYR 0.024 0.001 TYR H 107 PHE 0.014 0.001 PHE A 431 TRP 0.014 0.001 TRP B 400 HIS 0.007 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00466 (18800) covalent geometry : angle 0.67991 (25491) SS BOND : bond 0.00463 ( 22) SS BOND : angle 0.96007 ( 44) hydrogen bonds : bond 0.04468 ( 630) hydrogen bonds : angle 5.34038 ( 1650) Misc. bond : bond 0.00230 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 298 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.4589 (t) cc_final: 0.4302 (p) REVERT: H 116 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7120 (p) REVERT: L 94 TRP cc_start: 0.6441 (OUTLIER) cc_final: 0.4250 (t60) REVERT: A 350 GLN cc_start: 0.8380 (mp10) cc_final: 0.7998 (mp10) REVERT: A 394 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9097 (mmmm) REVERT: A 496 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7642 (tp) REVERT: D 25 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.5307 (p90) REVERT: D 74 TYR cc_start: 0.4761 (OUTLIER) cc_final: 0.2977 (m-80) REVERT: h 35 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8453 (m90) REVERT: h 80 TYR cc_start: 0.7986 (m-80) cc_final: 0.7528 (m-80) REVERT: h 93 VAL cc_start: 0.8084 (t) cc_final: 0.7851 (p) REVERT: l 91 ARG cc_start: 0.8511 (mmt90) cc_final: 0.7906 (mtt180) REVERT: B 140 MET cc_start: 0.8860 (mmm) cc_final: 0.8482 (mmm) REVERT: B 197 ASP cc_start: 0.8532 (t0) cc_final: 0.7872 (p0) REVERT: B 308 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8662 (m) REVERT: B 412 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8631 (mm-30) REVERT: B 433 SER cc_start: 0.9275 (t) cc_final: 0.9030 (p) REVERT: B 438 LEU cc_start: 0.8633 (mt) cc_final: 0.8418 (tt) REVERT: E 14 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9235 (p) REVERT: E 33 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 89 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9067 (mt0) REVERT: C 151 MET cc_start: 0.7780 (mmt) cc_final: 0.7500 (mmm) REVERT: C 197 ASP cc_start: 0.9073 (t0) cc_final: 0.8774 (t0) REVERT: C 286 SER cc_start: 0.9237 (p) cc_final: 0.9016 (p) REVERT: C 295 MET cc_start: 0.9370 (ptp) cc_final: 0.9100 (ptp) REVERT: C 307 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9387 (pp) REVERT: C 349 MET cc_start: 0.8288 (mmm) cc_final: 0.6598 (ptp) REVERT: C 358 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8536 (tt) REVERT: C 379 ASP cc_start: 0.9050 (t0) cc_final: 0.8710 (t0) REVERT: C 478 ASN cc_start: 0.8410 (m-40) cc_final: 0.8107 (m-40) REVERT: F 21 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: F 33 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8876 (tm-30) REVERT: 1 109 MET cc_start: -0.2504 (mtp) cc_final: -0.4242 (mpp) outliers start: 87 outliers final: 72 residues processed: 355 average time/residue: 0.1098 time to fit residues: 63.2391 Evaluate side-chains 382 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 298 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 35 HIS Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 2 residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 88 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 12 optimal weight: 40.0000 chunk 231 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 249 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116948 restraints weight = 36934.476| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.09 r_work: 0.3043 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18826 Z= 0.160 Angle : 0.657 11.063 25535 Z= 0.339 Chirality : 0.044 0.193 2848 Planarity : 0.005 0.095 3232 Dihedral : 5.422 54.395 2589 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.00 % Rotamer: Outliers : 4.55 % Allowed : 20.07 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2371 helix: 0.74 (0.26), residues: 423 sheet: 0.75 (0.20), residues: 793 loop : -1.63 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG l 91 TYR 0.022 0.001 TYR H 107 PHE 0.013 0.001 PHE E 42 TRP 0.015 0.001 TRP B 236 HIS 0.007 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00364 (18800) covalent geometry : angle 0.65627 (25491) SS BOND : bond 0.00397 ( 22) SS BOND : angle 0.86179 ( 44) hydrogen bonds : bond 0.04250 ( 630) hydrogen bonds : angle 5.30155 ( 1650) Misc. bond : bond 0.00192 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.34 seconds wall clock time: 76 minutes 57.25 seconds (4617.25 seconds total)