Starting phenix.real_space_refine on Mon Jun 16 02:44:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxg_27055/06_2025/8cxg_27055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxg_27055/06_2025/8cxg_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_27055/06_2025/8cxg_27055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxg_27055/06_2025/8cxg_27055.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxg_27055/06_2025/8cxg_27055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxg_27055/06_2025/8cxg_27055.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.23, per 1000 atoms: 0.56 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: 4.46 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.02 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: 5.61 Time building geometry restraints manager: 5.34 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: 3.960 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.340 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- 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 : 28.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP C 101 HIS 0.005 0.001 HIS C 288 PHE 0.015 0.002 PHE F 42 TYR 0.024 0.002 TYR E 25 ARG 0.006 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.14277 ( 630) hydrogen bonds : angle 6.90880 ( 1650) SS BOND : bond 0.35311 ( 22) SS BOND : angle 14.48709 ( 44) covalent geometry : bond 0.00828 (18800) covalent geometry : angle 0.96072 (25491) 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 : 2.119 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: 0.7390 (p) REVERT: H 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 466 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 349 MET cc_start: 0.6014 (mmm) cc_final: 0.4935 (ptp) REVERT: C 460 MET cc_start: 0.7468 (ptp) cc_final: 0.7185 (ptp) REVERT: 1 109 MET cc_start: 0.0576 (mtp) cc_final: -0.2075 (mtm) outliers start: 54 outliers final: 19 residues processed: 456 average time/residue: 0.3237 time to fit residues: 231.5141 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 : 2.713 ------------------------------------------------------------------------------- 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 198 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 213 optimal weight: 220.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 134 ASN A 148 HIS A 163 ASN 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 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 C 103 ASN C 134 ASN C 163 ASN C 350 GLN C 362 ASN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118146 restraints weight = 36649.249| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.19 r_work: 0.3100 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 18826 Z= 0.185 Angle : 0.731 18.330 25535 Z= 0.380 Chirality : 0.046 0.288 2848 Planarity : 0.006 0.130 3232 Dihedral : 6.473 59.222 2616 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.77 % Favored : 91.19 % Rotamer: Outliers : 3.79 % Allowed : 14.11 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2371 helix: 0.00 (0.24), residues: 435 sheet: -0.06 (0.18), residues: 825 loop : -2.14 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 94 HIS 0.008 0.001 HIS B 288 PHE 0.016 0.002 PHE C 431 TYR 0.015 0.001 TYR A 61 ARG 0.007 0.000 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 630) hydrogen bonds : angle 5.64533 ( 1650) SS BOND : bond 0.00419 ( 22) SS BOND : angle 1.17835 ( 44) covalent geometry : bond 0.00417 (18800) covalent geometry : angle 0.73047 (25491) Misc. bond : bond 0.00276 ( 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 418 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8624 (mmm) cc_final: 0.8243 (mmm) REVERT: H 57 SER cc_start: 0.4710 (t) cc_final: 0.4434 (p) REVERT: H 97 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7381 (m) REVERT: H 116 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7268 (p) REVERT: A 254 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8574 (p) REVERT: A 377 GLU cc_start: 0.8797 (pt0) cc_final: 0.8559 (pt0) REVERT: A 379 ASP cc_start: 0.8976 (t0) cc_final: 0.8769 (t0) REVERT: A 412 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8818 (mm-30) REVERT: A 498 LEU cc_start: 0.8432 (mp) cc_final: 0.8011 (mp) REVERT: D 25 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.5376 (p90) REVERT: h 93 VAL cc_start: 0.8202 (t) cc_final: 0.7989 (p) REVERT: B 68 MET cc_start: 0.8949 (mpp) cc_final: 0.8702 (mpp) REVERT: B 308 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 386 TYR cc_start: 0.9125 (m-80) cc_final: 0.8914 (m-80) REVERT: B 412 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8593 (mm-30) REVERT: B 473 MET cc_start: 0.8568 (tpp) cc_final: 0.8322 (tpp) REVERT: E 14 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9011 (p) REVERT: E 33 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 197 ASP cc_start: 0.8877 (t0) cc_final: 0.8367 (t0) REVERT: C 295 MET cc_start: 0.9408 (ptm) cc_final: 0.9194 (ptp) REVERT: C 349 MET cc_start: 0.7410 (mmm) cc_final: 0.5867 (ptp) REVERT: C 478 ASN cc_start: 0.8314 (m-40) cc_final: 0.8069 (m110) REVERT: F 33 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8817 (tm-30) REVERT: 1 109 MET cc_start: -0.2283 (mtp) cc_final: -0.3349 (mtm) outliers start: 75 outliers final: 33 residues processed: 392 average time/residue: 0.2572 time to fit residues: 161.5976 Evaluate side-chains 345 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 456 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL 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 143 VAL 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 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 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 F residue 34 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 172 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 214 optimal weight: 0.5980 chunk 149 optimal weight: 0.0980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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** D 7 HIS 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** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN C 148 HIS ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120755 restraints weight = 36870.883| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.26 r_work: 0.3139 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18826 Z= 0.130 Angle : 0.638 11.616 25535 Z= 0.335 Chirality : 0.044 0.257 2848 Planarity : 0.005 0.105 3232 Dihedral : 5.595 55.175 2593 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.65 % Favored : 91.31 % Rotamer: Outliers : 3.99 % Allowed : 16.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2371 helix: 0.52 (0.26), residues: 422 sheet: 0.30 (0.19), residues: 803 loop : -1.88 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 400 HIS 0.005 0.001 HIS C 288 PHE 0.015 0.001 PHE F 42 TYR 0.013 0.001 TYR A 61 ARG 0.008 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 630) hydrogen bonds : angle 5.36419 ( 1650) SS BOND : bond 0.00403 ( 22) SS BOND : angle 0.86466 ( 44) covalent geometry : bond 0.00282 (18800) covalent geometry : angle 0.63769 (25491) Misc. bond : bond 0.00145 ( 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 413 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 334 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8705 (mmm) cc_final: 0.8326 (mmm) REVERT: H 57 SER cc_start: 0.3794 (t) cc_final: 0.3498 (p) REVERT: H 97 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7598 (m) REVERT: L 94 TRP cc_start: 0.6576 (OUTLIER) cc_final: 0.4756 (t60) REVERT: A 197 ASP cc_start: 0.8861 (t0) cc_final: 0.8652 (t0) REVERT: A 254 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 350 GLN cc_start: 0.8014 (mp10) cc_final: 0.7755 (mp10) REVERT: A 394 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9247 (mmmm) REVERT: A 412 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8765 (mm-30) REVERT: D 25 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.5415 (p90) REVERT: h 60 TYR cc_start: 0.8370 (m-80) cc_final: 0.8055 (m-80) REVERT: h 93 VAL cc_start: 0.8155 (t) cc_final: 0.7937 (p) REVERT: l 91 ARG cc_start: 0.8396 (mmt90) cc_final: 0.8028 (mmt90) REVERT: B 36 GLN cc_start: 0.8809 (tp40) cc_final: 0.8580 (tp40) REVERT: B 68 MET cc_start: 0.8894 (mpp) cc_final: 0.8638 (mpp) REVERT: B 197 ASP cc_start: 0.8225 (t0) cc_final: 0.7853 (p0) REVERT: B 308 CYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 377 GLU cc_start: 0.9014 (pt0) cc_final: 0.8635 (tt0) REVERT: B 412 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8564 (mm-30) REVERT: B 477 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8594 (mp) REVERT: E 14 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9152 (p) REVERT: E 33 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 197 ASP cc_start: 0.8930 (t0) cc_final: 0.8471 (t0) REVERT: C 307 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9235 (pp) REVERT: C 349 MET cc_start: 0.7709 (mmm) cc_final: 0.6188 (ptp) REVERT: C 379 ASP cc_start: 0.8912 (t0) cc_final: 0.8599 (t0) REVERT: C 474 TRP cc_start: 0.8410 (t-100) cc_final: 0.8089 (t-100) REVERT: C 478 ASN cc_start: 0.8530 (m-40) cc_final: 0.7999 (m-40) REVERT: F 33 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8760 (tm-30) REVERT: 1 109 MET cc_start: -0.2341 (mtp) cc_final: -0.3387 (mtm) outliers start: 79 outliers final: 46 residues processed: 385 average time/residue: 0.3429 time to fit residues: 215.4676 Evaluate side-chains 362 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 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 189 ASP 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 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 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 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 31 VAL Chi-restraints excluded: chain B residue 143 VAL 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 456 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU 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 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 284 LEU 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 1 residue 35 HIS 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 160 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 38 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN B 144 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117838 restraints weight = 36951.701| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.22 r_work: 0.3085 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 18826 Z= 0.200 Angle : 0.667 12.441 25535 Z= 0.347 Chirality : 0.045 0.267 2848 Planarity : 0.005 0.098 3232 Dihedral : 5.560 56.556 2592 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 4.90 % Allowed : 16.73 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2371 helix: 0.57 (0.26), residues: 429 sheet: 0.38 (0.19), residues: 808 loop : -1.75 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 400 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE A 431 TYR 0.014 0.001 TYR A 61 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 630) hydrogen bonds : angle 5.28602 ( 1650) SS BOND : bond 0.00450 ( 22) SS BOND : angle 0.92730 ( 44) covalent geometry : bond 0.00455 (18800) covalent geometry : angle 0.66667 (25491) Misc. bond : bond 0.00218 ( 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 417 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 320 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 SER cc_start: 0.4578 (t) cc_final: 0.4251 (p) REVERT: H 95 TYR cc_start: 0.7445 (m-80) cc_final: 0.7191 (m-80) REVERT: H 116 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7488 (p) REVERT: L 94 TRP cc_start: 0.6645 (OUTLIER) cc_final: 0.4757 (t60) REVERT: A 350 GLN cc_start: 0.8017 (mp10) cc_final: 0.7694 (mp10) REVERT: A 412 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8820 (mm-30) REVERT: A 473 MET cc_start: 0.8269 (mmm) cc_final: 0.8051 (mmm) REVERT: D 25 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.5486 (p90) REVERT: h 60 TYR cc_start: 0.8304 (m-80) cc_final: 0.7972 (m-80) REVERT: h 93 VAL cc_start: 0.8154 (t) cc_final: 0.7931 (p) REVERT: l 91 ARG cc_start: 0.8429 (mmt90) cc_final: 0.7929 (mtt180) REVERT: B 36 GLN cc_start: 0.8945 (tp40) cc_final: 0.8715 (tp40) REVERT: B 68 MET cc_start: 0.8971 (mpp) cc_final: 0.8710 (mpp) REVERT: B 140 MET cc_start: 0.8960 (mmm) cc_final: 0.8614 (mmm) REVERT: B 197 ASP cc_start: 0.8446 (t0) cc_final: 0.7891 (p0) REVERT: B 308 CYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8647 (m) REVERT: B 345 MET cc_start: 0.9081 (mtp) cc_final: 0.8856 (mtm) REVERT: B 349 MET cc_start: 0.8825 (mmt) cc_final: 0.8430 (mmt) REVERT: B 377 GLU cc_start: 0.9120 (pt0) cc_final: 0.8847 (tt0) REVERT: B 412 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8587 (mm-30) REVERT: B 477 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8579 (mp) REVERT: E 14 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9147 (p) REVERT: E 30 ILE cc_start: 0.9062 (mt) cc_final: 0.8842 (mt) REVERT: E 33 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 197 ASP cc_start: 0.8990 (t0) cc_final: 0.8554 (t0) REVERT: C 307 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9277 (pp) REVERT: C 349 MET cc_start: 0.7917 (mmm) cc_final: 0.6405 (ptp) REVERT: C 379 ASP cc_start: 0.8960 (t0) cc_final: 0.8565 (t0) REVERT: C 473 MET cc_start: 0.8711 (mmm) cc_final: 0.8426 (mmt) REVERT: C 474 TRP cc_start: 0.8522 (t-100) cc_final: 0.8091 (t-100) REVERT: C 478 ASN cc_start: 0.8447 (m-40) cc_final: 0.7841 (m-40) REVERT: F 33 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8768 (tm-30) REVERT: 1 109 MET cc_start: -0.2456 (mtp) cc_final: -0.3904 (mtm) outliers start: 97 outliers final: 58 residues processed: 383 average time/residue: 0.2714 time to fit residues: 166.5448 Evaluate side-chains 378 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 5 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 65 ILE 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 A residue 475 LEU Chi-restraints excluded: chain A residue 495 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 63 SER 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 85 GLN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 GLU 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 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 466 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 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 396 ILE Chi-restraints excluded: chain C residue 460 MET 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 1 residue 35 HIS 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 24 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 0 optimal weight: 60.0000 chunk 93 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 216 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 85 GLN B 163 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** 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 = 0.3845 r_free = 0.3845 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.114970 restraints weight = 37410.517| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.11 r_work: 0.3019 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18826 Z= 0.253 Angle : 0.695 13.680 25535 Z= 0.362 Chirality : 0.046 0.280 2848 Planarity : 0.005 0.091 3232 Dihedral : 5.675 58.255 2591 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.91 % Favored : 90.05 % Rotamer: Outliers : 5.46 % Allowed : 17.24 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2371 helix: 0.58 (0.26), residues: 427 sheet: 0.43 (0.19), residues: 813 loop : -1.74 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 400 HIS 0.006 0.001 HIS A 288 PHE 0.016 0.001 PHE A 431 TYR 0.025 0.002 TYR H 105 ARG 0.004 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 630) hydrogen bonds : angle 5.32411 ( 1650) SS BOND : bond 0.00515 ( 22) SS BOND : angle 1.07724 ( 44) covalent geometry : bond 0.00576 (18800) covalent geometry : angle 0.69412 (25491) Misc. bond : bond 0.00277 ( 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 409 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 301 time to evaluate : 2.129 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: H 57 SER cc_start: 0.4400 (t) cc_final: 0.4050 (p) REVERT: H 116 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7358 (p) REVERT: L 94 TRP cc_start: 0.6662 (OUTLIER) cc_final: 0.4755 (t60) REVERT: A 350 GLN cc_start: 0.8055 (mp10) cc_final: 0.7634 (mp10) REVERT: A 412 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8867 (mm-30) REVERT: D 25 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.5406 (p90) REVERT: h 80 TYR cc_start: 0.7917 (m-80) cc_final: 0.7466 (m-80) REVERT: h 93 VAL cc_start: 0.8105 (t) cc_final: 0.7881 (p) REVERT: l 91 ARG cc_start: 0.8539 (mmt90) cc_final: 0.8104 (mtt180) REVERT: B 36 GLN cc_start: 0.9052 (tp40) cc_final: 0.8818 (tp40) REVERT: B 140 MET cc_start: 0.8991 (mmm) cc_final: 0.8613 (mmm) REVERT: B 197 ASP cc_start: 0.8443 (t0) cc_final: 0.7913 (p0) REVERT: B 308 CYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8667 (m) REVERT: B 349 MET cc_start: 0.8835 (mmt) cc_final: 0.8455 (mmt) REVERT: B 412 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8614 (mm-30) REVERT: B 477 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8591 (mp) REVERT: E 14 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9162 (p) REVERT: E 33 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 69 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 89 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9033 (tt0) REVERT: C 197 ASP cc_start: 0.9012 (t0) cc_final: 0.8474 (t0) REVERT: C 286 SER cc_start: 0.9244 (p) cc_final: 0.8999 (p) REVERT: C 307 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9352 (pp) REVERT: C 349 MET cc_start: 0.8289 (mmm) cc_final: 0.6480 (ptp) REVERT: C 379 ASP cc_start: 0.9014 (t0) cc_final: 0.8635 (t0) REVERT: C 474 TRP cc_start: 0.8590 (t-100) cc_final: 0.8181 (t-100) REVERT: C 478 ASN cc_start: 0.8364 (m-40) cc_final: 0.7912 (m-40) REVERT: 1 109 MET cc_start: -0.2294 (mtp) cc_final: -0.3714 (mtm) outliers start: 108 outliers final: 69 residues processed: 372 average time/residue: 0.2580 time to fit residues: 154.0495 Evaluate side-chains 375 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 297 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 5 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 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 288 HIS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 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 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 83 MET 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 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 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 466 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 E residue 65 VAL Chi-restraints excluded: chain E residue 69 LEU 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 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 365 ILE 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 1 residue 35 HIS 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 193 optimal weight: 6.9990 chunk 115 optimal weight: 0.0000 chunk 119 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- 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 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 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 = 0.3879 r_free = 0.3879 target = 0.157624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117750 restraints weight = 37355.094| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.18 r_work: 0.3045 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18826 Z= 0.176 Angle : 0.652 12.325 25535 Z= 0.338 Chirality : 0.044 0.279 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.522 55.683 2590 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.19 % Favored : 90.76 % Rotamer: Outliers : 4.45 % Allowed : 19.06 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2371 helix: 0.74 (0.26), residues: 419 sheet: 0.45 (0.19), residues: 809 loop : -1.67 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 400 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE F 42 TYR 0.024 0.001 TYR H 105 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 630) hydrogen bonds : angle 5.26830 ( 1650) SS BOND : bond 0.00401 ( 22) SS BOND : angle 0.89897 ( 44) covalent geometry : bond 0.00402 (18800) covalent geometry : angle 0.65135 (25491) Misc. bond : bond 0.00205 ( 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 395 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 307 time to evaluate : 1.867 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: H 57 SER cc_start: 0.3149 (t) cc_final: 0.2916 (p) REVERT: H 116 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7422 (p) REVERT: L 94 TRP cc_start: 0.6451 (OUTLIER) cc_final: 0.4445 (t60) REVERT: A 294 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9096 (mtmm) REVERT: A 350 GLN cc_start: 0.8149 (mp10) cc_final: 0.7714 (mp10) REVERT: A 412 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8904 (mm-30) REVERT: A 496 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7512 (tp) REVERT: D 25 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.5271 (p90) REVERT: D 74 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.2964 (m-80) REVERT: h 60 TYR cc_start: 0.8342 (m-80) cc_final: 0.8069 (m-80) REVERT: h 93 VAL cc_start: 0.8048 (t) cc_final: 0.7823 (p) REVERT: h 107 TYR cc_start: 0.9425 (p90) cc_final: 0.9214 (p90) REVERT: l 91 ARG cc_start: 0.8470 (mmt90) cc_final: 0.8014 (mtt180) REVERT: B 140 MET cc_start: 0.8972 (mmm) cc_final: 0.8558 (mmm) REVERT: B 197 ASP cc_start: 0.8458 (t0) cc_final: 0.7910 (p0) REVERT: B 308 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8639 (m) REVERT: B 377 GLU cc_start: 0.9136 (pt0) cc_final: 0.8897 (tt0) REVERT: B 412 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8575 (mm-30) REVERT: B 433 SER cc_start: 0.9046 (t) cc_final: 0.8793 (p) REVERT: B 477 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8574 (mp) REVERT: E 14 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9133 (p) REVERT: E 30 ILE cc_start: 0.9094 (mt) cc_final: 0.8848 (mt) REVERT: E 33 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 89 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9010 (tt0) REVERT: C 197 ASP cc_start: 0.9044 (t0) cc_final: 0.8584 (t0) REVERT: C 286 SER cc_start: 0.9236 (p) cc_final: 0.8996 (p) REVERT: C 295 MET cc_start: 0.9383 (ptp) cc_final: 0.9043 (ptp) REVERT: C 307 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9312 (pp) REVERT: C 349 MET cc_start: 0.8322 (mmm) cc_final: 0.6531 (ptp) REVERT: C 379 ASP cc_start: 0.9142 (t0) cc_final: 0.8549 (t0) REVERT: C 474 TRP cc_start: 0.8512 (t-100) cc_final: 0.8088 (t-100) REVERT: C 478 ASN cc_start: 0.8357 (m-40) cc_final: 0.7869 (m-40) REVERT: 1 109 MET cc_start: -0.2193 (mtp) cc_final: -0.3625 (mtm) outliers start: 88 outliers final: 64 residues processed: 363 average time/residue: 0.2548 time to fit residues: 147.8098 Evaluate side-chains 377 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU 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 22 SER Chi-restraints excluded: chain L residue 30 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 65 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 495 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 63 SER 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 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 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 466 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 E residue 52 LEU 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 C residue 498 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS 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 22 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 213 optimal weight: 320.0000 chunk 84 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 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** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 HIS l 90 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 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 = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115791 restraints weight = 37167.357| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.09 r_work: 0.3027 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18826 Z= 0.237 Angle : 0.689 15.221 25535 Z= 0.356 Chirality : 0.046 0.278 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.594 56.904 2590 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.16 % Favored : 89.79 % Rotamer: Outliers : 5.21 % Allowed : 18.86 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2371 helix: 0.69 (0.26), residues: 419 sheet: 0.49 (0.19), residues: 807 loop : -1.67 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 400 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE A 431 TYR 0.024 0.001 TYR H 107 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 630) hydrogen bonds : angle 5.27565 ( 1650) SS BOND : bond 0.00496 ( 22) SS BOND : angle 1.00931 ( 44) covalent geometry : bond 0.00543 (18800) covalent geometry : angle 0.68812 (25491) Misc. bond : bond 0.00256 ( 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 394 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 291 time to evaluate : 2.122 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: H 116 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7536 (p) REVERT: L 94 TRP cc_start: 0.6442 (OUTLIER) cc_final: 0.4408 (t60) REVERT: A 294 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9053 (mtmm) REVERT: A 350 GLN cc_start: 0.8265 (mp10) cc_final: 0.7881 (mp10) REVERT: A 412 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8903 (mm-30) REVERT: A 496 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7460 (tp) REVERT: D 25 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.5340 (p90) REVERT: D 74 TYR cc_start: 0.4791 (OUTLIER) cc_final: 0.3038 (m-80) REVERT: h 93 VAL cc_start: 0.7775 (t) cc_final: 0.7563 (p) REVERT: h 107 TYR cc_start: 0.9441 (p90) cc_final: 0.9199 (p90) REVERT: l 91 ARG cc_start: 0.8496 (mmt90) cc_final: 0.7983 (mtt180) REVERT: B 140 MET cc_start: 0.8972 (mmm) cc_final: 0.8541 (mmm) REVERT: B 197 ASP cc_start: 0.8487 (t0) cc_final: 0.7923 (p0) REVERT: B 308 CYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 412 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8644 (mm-30) REVERT: B 438 LEU cc_start: 0.8574 (mt) cc_final: 0.8243 (tp) REVERT: B 473 MET cc_start: 0.8634 (tpp) cc_final: 0.8323 (tpp) REVERT: B 477 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 491 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7177 (tp) REVERT: E 14 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9176 (p) REVERT: E 33 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 69 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 89 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9037 (tt0) REVERT: C 151 MET cc_start: 0.7857 (mmt) cc_final: 0.7523 (mmm) REVERT: C 197 ASP cc_start: 0.9058 (t0) cc_final: 0.8562 (t0) REVERT: C 286 SER cc_start: 0.9261 (p) cc_final: 0.9003 (p) REVERT: C 307 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9390 (pp) REVERT: C 349 MET cc_start: 0.8376 (mmm) cc_final: 0.6576 (ptp) REVERT: C 379 ASP cc_start: 0.9141 (t0) cc_final: 0.8573 (t0) REVERT: C 474 TRP cc_start: 0.8538 (t-100) cc_final: 0.8124 (t-100) REVERT: C 478 ASN cc_start: 0.8393 (m-40) cc_final: 0.7952 (m-40) REVERT: F 21 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: 1 109 MET cc_start: -0.2493 (mtp) cc_final: -0.3954 (mpp) outliers start: 103 outliers final: 72 residues processed: 354 average time/residue: 0.2626 time to fit residues: 149.3350 Evaluate side-chains 375 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU 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 5 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 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 288 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 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 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR 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 79 GLU 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 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 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 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 69 LEU 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 C residue 498 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS 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 173 optimal weight: 0.2980 chunk 200 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 27 optimal weight: 0.0770 chunk 81 optimal weight: 50.0000 chunk 136 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 overall best weight: 4.4744 ------------------------------------------------------------------------------- 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 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117250 restraints weight = 36858.214| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.15 r_work: 0.3043 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18826 Z= 0.168 Angle : 0.649 12.822 25535 Z= 0.335 Chirality : 0.044 0.223 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.440 54.209 2590 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.55 % Rotamer: Outliers : 4.95 % Allowed : 19.62 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2371 helix: 0.71 (0.26), residues: 419 sheet: 0.63 (0.19), residues: 793 loop : -1.65 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP l 94 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE F 42 TYR 0.023 0.001 TYR H 107 ARG 0.005 0.000 ARG l 91 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 630) hydrogen bonds : angle 5.21948 ( 1650) SS BOND : bond 0.00385 ( 22) SS BOND : angle 0.85383 ( 44) covalent geometry : bond 0.00384 (18800) covalent geometry : angle 0.64853 (25491) Misc. bond : bond 0.00203 ( 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 397 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 299 time to evaluate : 1.839 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: H 57 SER cc_start: 0.3637 (t) cc_final: 0.3403 (p) REVERT: H 116 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7176 (p) REVERT: L 94 TRP cc_start: 0.6278 (OUTLIER) cc_final: 0.4147 (t60) REVERT: A 294 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9041 (mtmm) REVERT: A 317 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8199 (pt) REVERT: A 350 GLN cc_start: 0.8276 (mp10) cc_final: 0.7863 (mp10) REVERT: A 412 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8929 (mm-30) REVERT: A 473 MET cc_start: 0.9031 (tpp) cc_final: 0.8721 (mmm) REVERT: D 25 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.5259 (p90) REVERT: D 74 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.2914 (m-80) REVERT: h 93 VAL cc_start: 0.8017 (t) cc_final: 0.7786 (p) REVERT: h 107 TYR cc_start: 0.9420 (p90) cc_final: 0.9211 (p90) REVERT: l 91 ARG cc_start: 0.8473 (mmt90) cc_final: 0.8090 (mtt-85) REVERT: B 140 MET cc_start: 0.8913 (mmm) cc_final: 0.8499 (mmm) REVERT: B 197 ASP cc_start: 0.8480 (t0) cc_final: 0.7897 (p0) REVERT: B 308 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8684 (m) REVERT: B 374 MET cc_start: 0.9003 (ppp) cc_final: 0.8652 (ppp) REVERT: B 412 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8598 (mm-30) REVERT: B 438 LEU cc_start: 0.8591 (mt) cc_final: 0.8281 (tp) REVERT: B 477 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 491 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7371 (mt) REVERT: B 500 THR cc_start: 0.8098 (t) cc_final: 0.7871 (p) REVERT: E 14 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.9137 (p) REVERT: E 33 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 89 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8983 (mt0) REVERT: C 151 MET cc_start: 0.7646 (mmt) cc_final: 0.7346 (mmm) REVERT: C 197 ASP cc_start: 0.9076 (t0) cc_final: 0.8615 (t0) REVERT: C 286 SER cc_start: 0.9235 (p) cc_final: 0.8997 (p) REVERT: C 307 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9346 (pp) REVERT: C 349 MET cc_start: 0.8280 (mmm) cc_final: 0.6607 (ptp) REVERT: C 379 ASP cc_start: 0.9138 (t0) cc_final: 0.8572 (t0) REVERT: C 474 TRP cc_start: 0.8530 (t-100) cc_final: 0.8083 (t-100) REVERT: C 478 ASN cc_start: 0.8383 (m-40) cc_final: 0.7891 (m-40) REVERT: F 21 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: 1 109 MET cc_start: -0.2458 (mtp) cc_final: -0.4167 (mpp) outliers start: 98 outliers final: 75 residues processed: 359 average time/residue: 0.2497 time to fit residues: 144.4370 Evaluate side-chains 380 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 292 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 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 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 276 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 495 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 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 22 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 79 GLU 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 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 385 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 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 E residue 52 LEU 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 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 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS 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 136 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117844 restraints weight = 37206.077| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.17 r_work: 0.3050 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18826 Z= 0.156 Angle : 0.644 13.444 25535 Z= 0.332 Chirality : 0.044 0.204 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.339 52.691 2590 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.55 % Rotamer: Outliers : 4.45 % Allowed : 20.42 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2371 helix: 0.75 (0.26), residues: 419 sheet: 0.62 (0.19), residues: 802 loop : -1.60 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP l 94 HIS 0.004 0.001 HIS A 288 PHE 0.014 0.001 PHE F 42 TYR 0.022 0.001 TYR H 107 ARG 0.005 0.000 ARG F 31 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 630) hydrogen bonds : angle 5.16217 ( 1650) SS BOND : bond 0.00369 ( 22) SS BOND : angle 0.83741 ( 44) covalent geometry : bond 0.00357 (18800) covalent geometry : angle 0.64393 (25491) Misc. bond : bond 0.00176 ( 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 384 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 296 time to evaluate : 2.208 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: 0.3514 (t) cc_final: 0.3285 (p) REVERT: H 116 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7206 (p) REVERT: L 94 TRP cc_start: 0.6355 (OUTLIER) cc_final: 0.4179 (t60) REVERT: A 294 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9049 (mtmm) REVERT: A 317 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8242 (pt) REVERT: A 350 GLN cc_start: 0.8267 (mp10) cc_final: 0.7835 (mp10) REVERT: A 412 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8929 (mm-30) REVERT: A 473 MET cc_start: 0.9032 (tpp) cc_final: 0.8740 (mmm) REVERT: D 25 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.5224 (p90) REVERT: D 74 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.2975 (m-80) REVERT: h 80 TYR cc_start: 0.8001 (m-80) cc_final: 0.7540 (m-80) REVERT: h 93 VAL cc_start: 0.8041 (t) cc_final: 0.7808 (p) REVERT: l 91 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8100 (mtt180) REVERT: B 140 MET cc_start: 0.8905 (mmm) cc_final: 0.8489 (mmm) REVERT: B 197 ASP cc_start: 0.8464 (t0) cc_final: 0.7892 (p0) REVERT: B 308 CYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8670 (m) REVERT: B 374 MET cc_start: 0.9028 (ppp) cc_final: 0.8676 (ppp) REVERT: B 412 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8586 (mm-30) REVERT: B 438 LEU cc_start: 0.8576 (mt) cc_final: 0.8355 (tt) REVERT: B 477 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8558 (mp) REVERT: E 14 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9141 (p) REVERT: E 33 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 89 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8975 (mt0) REVERT: C 151 MET cc_start: 0.7628 (mmt) cc_final: 0.7340 (mmm) REVERT: C 197 ASP cc_start: 0.9083 (t0) cc_final: 0.8728 (t0) REVERT: C 286 SER cc_start: 0.9188 (p) cc_final: 0.8939 (p) REVERT: C 307 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9368 (pp) REVERT: C 349 MET cc_start: 0.8252 (mmm) cc_final: 0.6590 (ptp) REVERT: C 358 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8425 (tt) REVERT: C 379 ASP cc_start: 0.9136 (t0) cc_final: 0.8584 (t0) REVERT: C 474 TRP cc_start: 0.8513 (t-100) cc_final: 0.8091 (t-100) REVERT: C 478 ASN cc_start: 0.8379 (m-40) cc_final: 0.7889 (m-40) REVERT: F 21 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: 1 83 MET cc_start: 0.6491 (ptm) cc_final: 0.6275 (ptm) REVERT: 1 109 MET cc_start: -0.2382 (mtp) cc_final: -0.4081 (mpp) outliers start: 88 outliers final: 71 residues processed: 350 average time/residue: 0.2726 time to fit residues: 153.1616 Evaluate side-chains 375 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 291 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 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 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 495 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 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 22 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 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 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 385 SER 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 E residue 38 ARG Chi-restraints excluded: chain E residue 52 LEU 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 317 ILE 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 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 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS 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 86 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 116 optimal weight: 0.0030 chunk 9 optimal weight: 20.0000 chunk 190 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.3998 ------------------------------------------------------------------------------- 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 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118975 restraints weight = 37119.787| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.14 r_work: 0.3055 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18826 Z= 0.166 Angle : 0.653 11.799 25535 Z= 0.335 Chirality : 0.044 0.203 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.340 52.248 2590 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.55 % Rotamer: Outliers : 4.60 % Allowed : 20.22 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2371 helix: 0.72 (0.26), residues: 419 sheet: 0.63 (0.19), residues: 802 loop : -1.58 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 101 HIS 0.005 0.001 HIS C 210 PHE 0.013 0.001 PHE F 42 TYR 0.022 0.001 TYR H 107 ARG 0.005 0.000 ARG l 91 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 630) hydrogen bonds : angle 5.18148 ( 1650) SS BOND : bond 0.00391 ( 22) SS BOND : angle 0.85539 ( 44) covalent geometry : bond 0.00381 (18800) covalent geometry : angle 0.65294 (25491) Misc. bond : bond 0.00181 ( 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 382 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 291 time to evaluate : 1.982 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: H 57 SER cc_start: 0.3174 (t) cc_final: 0.2941 (p) REVERT: H 116 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7259 (p) REVERT: L 94 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.4152 (t60) REVERT: A 277 MET cc_start: 0.8807 (mtt) cc_final: 0.8566 (tpp) REVERT: A 294 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9031 (mtmm) REVERT: A 317 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8277 (pt) REVERT: A 350 GLN cc_start: 0.8278 (mp10) cc_final: 0.7837 (mp10) REVERT: A 473 MET cc_start: 0.9045 (tpp) cc_final: 0.8755 (mmm) REVERT: D 25 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.5259 (p90) REVERT: D 31 ARG cc_start: 0.6221 (mmt180) cc_final: 0.5590 (mtt90) REVERT: D 74 TYR cc_start: 0.4740 (OUTLIER) cc_final: 0.3029 (m-80) REVERT: h 80 TYR cc_start: 0.8093 (m-80) cc_final: 0.7619 (m-80) REVERT: h 93 VAL cc_start: 0.8092 (t) cc_final: 0.7855 (p) REVERT: l 91 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8003 (mtt180) REVERT: B 140 MET cc_start: 0.8877 (mmm) cc_final: 0.8476 (mmm) REVERT: B 197 ASP cc_start: 0.8443 (t0) cc_final: 0.7895 (p0) REVERT: B 308 CYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8673 (m) REVERT: B 374 MET cc_start: 0.9024 (ppp) cc_final: 0.8695 (ppp) REVERT: B 412 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8599 (mm-30) REVERT: B 473 MET cc_start: 0.8453 (tpp) cc_final: 0.8060 (mmt) REVERT: B 477 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8590 (mp) REVERT: E 14 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9131 (p) REVERT: E 33 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 89 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8946 (mt0) REVERT: C 151 MET cc_start: 0.7695 (mmt) cc_final: 0.7413 (mmm) REVERT: C 286 SER cc_start: 0.9168 (p) cc_final: 0.8923 (p) REVERT: C 307 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9377 (pp) REVERT: C 349 MET cc_start: 0.8274 (mmm) cc_final: 0.6593 (ptp) REVERT: C 358 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8460 (tt) REVERT: C 379 ASP cc_start: 0.9132 (t0) cc_final: 0.8603 (t0) REVERT: C 474 TRP cc_start: 0.8513 (t-100) cc_final: 0.8155 (t-100) REVERT: C 478 ASN cc_start: 0.8400 (m-40) cc_final: 0.7918 (m-40) REVERT: F 21 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: 1 83 MET cc_start: 0.6493 (ptm) cc_final: 0.6273 (ptm) REVERT: 1 109 MET cc_start: -0.2260 (mtp) cc_final: -0.4044 (mpp) outliers start: 91 outliers final: 74 residues processed: 348 average time/residue: 0.2532 time to fit residues: 142.2011 Evaluate side-chains 376 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 63 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 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 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 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 35 HIS Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 22 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 79 GLU 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 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 385 SER 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 E residue 52 LEU 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 317 ILE 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 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 55 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS 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 26 optimal weight: 10.0000 chunk 224 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.115772 restraints weight = 36209.057| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.12 r_work: 0.3013 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3656 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= 0.234 Angle : 0.692 12.525 25535 Z= 0.357 Chirality : 0.046 0.206 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.498 54.975 2590 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.04 % Favored : 89.92 % Rotamer: Outliers : 4.65 % Allowed : 20.32 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2371 helix: 0.67 (0.26), residues: 419 sheet: 0.59 (0.19), residues: 802 loop : -1.58 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 101 HIS 0.005 0.001 HIS A 288 PHE 0.015 0.001 PHE A 431 TYR 0.024 0.001 TYR H 107 ARG 0.006 0.000 ARG l 91 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 630) hydrogen bonds : angle 5.24704 ( 1650) SS BOND : bond 0.00494 ( 22) SS BOND : angle 1.00805 ( 44) covalent geometry : bond 0.00537 (18800) covalent geometry : angle 0.69094 (25491) Misc. bond : bond 0.00231 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9807.80 seconds wall clock time: 170 minutes 52.80 seconds (10252.80 seconds total)