Starting phenix.real_space_refine on Wed Mar 4 20:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxh_27056/03_2026/8cxh_27056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxh_27056/03_2026/8cxh_27056.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/8cxh_27056/03_2026/8cxh_27056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxh_27056/03_2026/8cxh_27056.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxh_27056/03_2026/8cxh_27056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxh_27056/03_2026/8cxh_27056.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 10511 2.51 5 N 2866 2.21 5 O 3147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16634 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3714 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3714 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} 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: "h" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "l" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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} Time building chain proxies: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16634 At special positions: 0 Unit cell: (106, 202.46, 120.84, 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 110 16.00 O 3147 8.00 N 2866 7.00 C 10511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=1.69 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=1.75 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.50 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=1.85 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=1.47 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 826.3 milliseconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 30 sheets defined 23.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.868A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.583A pdb=" N THR A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.545A pdb=" N PHE A 431 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 500 Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.004A pdb=" N THR D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 56 through 74 Proline residue: D 72 - end of helix 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 61 through 64 removed outlier: 3.719A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 3 through 7 removed outlier: 4.631A pdb=" N SER B 7 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.859A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.549A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 426 through 431 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 501 removed outlier: 4.351A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.560A pdb=" N LYS E 11 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.997A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' 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 61 through 64 removed outlier: 3.552A pdb=" N GLN h 64 " --> pdb=" O GLN h 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 64' Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.649A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.538A pdb=" N ILE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL C 153 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 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 removed outlier: 3.670A pdb=" N PHE C 431 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 461 through 479 Processing helix chain 'C' and resid 483 through 500 Processing helix chain 'F' and resid 6 through 11 removed outlier: 3.945A pdb=" N THR F 9 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.971A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 71 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.509A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 110 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: 4.078A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 26 removed outlier: 4.332A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASP A 296 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER A 185 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 312 through 314 current: chain 'A' and resid 326 through 332 Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.556A 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 50 current: chain 'B' and resid 126 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 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: 3.964A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.438A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 73 removed outlier: 5.031A pdb=" N ILE B 65 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 120 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 67 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 118 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 112 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB8, first strand: chain 'B' and resid 312 through 320 removed outlier: 6.761A pdb=" N THR B 315 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLN B 331 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE B 317 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 329 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'B' and resid 353 through 354 removed outlier: 4.582A pdb=" N THR B 353 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 347 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'h' and resid 10 through 12 removed outlier: 7.443A pdb=" N TYR h 32 " --> pdb=" O ASN h 52 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN h 52 " --> pdb=" O TYR h 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET h 34 " --> pdb=" O TRP h 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'l' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 9 through 12 current: chain 'l' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 45 through 48 current: chain 'l' and resid 96 through 98 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'l' and resid 19 through 24 Processing sheet with id=AC7, 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 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 110 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: 4.346A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 273 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 21 through 26 removed outlier: 5.398A pdb=" N ASP C 296 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER C 185 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AD1, 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=AD2, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AD3, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.646A pdb=" N THR C 353 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 347 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET C 345 " --> pdb=" O VAL C 355 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1557 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: 2.72 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 2706 1.27 - 1.42: 4401 1.42 - 1.56: 9726 1.56 - 1.71: 0 1.71 - 1.86: 173 Bond restraints: 17006 Sorted by residual: bond pdb=" CA ASN C 238 " pdb=" C ASN C 238 " ideal model delta sigma weight residual 1.526 1.378 0.148 9.20e-03 1.18e+04 2.58e+02 bond pdb=" C ASN C 238 " pdb=" O ASN C 238 " ideal model delta sigma weight residual 1.234 1.121 0.113 8.30e-03 1.45e+04 1.86e+02 bond pdb=" CA HIS C 249 " pdb=" C HIS C 249 " ideal model delta sigma weight residual 1.524 1.408 0.115 1.35e-02 5.49e+03 7.28e+01 bond pdb=" CA ARG C 252 " pdb=" C ARG C 252 " ideal model delta sigma weight residual 1.527 1.449 0.079 9.80e-03 1.04e+04 6.43e+01 bond pdb=" C ARG C 252 " pdb=" O ARG C 252 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.06e-02 8.90e+03 6.20e+01 ... (remaining 17001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 22818 3.42 - 6.83: 195 6.83 - 10.25: 21 10.25 - 13.67: 7 13.67 - 17.08: 5 Bond angle restraints: 23046 Sorted by residual: angle pdb=" N LYS C 251 " pdb=" CA LYS C 251 " pdb=" C LYS C 251 " ideal model delta sigma weight residual 111.36 123.90 -12.54 1.09e+00 8.42e-01 1.32e+02 angle pdb=" C ASN C 362 " pdb=" N PRO C 363 " pdb=" CA PRO C 363 " ideal model delta sigma weight residual 119.84 107.84 12.00 1.25e+00 6.40e-01 9.21e+01 angle pdb=" N THR C 360 " pdb=" CA THR C 360 " pdb=" C THR C 360 " ideal model delta sigma weight residual 107.20 92.33 14.87 1.70e+00 3.46e-01 7.65e+01 angle pdb=" CA TRP C 101 " pdb=" CB TRP C 101 " pdb=" CG TRP C 101 " ideal model delta sigma weight residual 113.60 129.36 -15.76 1.90e+00 2.77e-01 6.88e+01 angle pdb=" N PHE B 463 " pdb=" CA PHE B 463 " pdb=" C PHE B 463 " ideal model delta sigma weight residual 112.72 102.26 10.46 1.28e+00 6.10e-01 6.68e+01 ... (remaining 23041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 9203 17.53 - 35.05: 634 35.05 - 52.58: 125 52.58 - 70.11: 38 70.11 - 87.63: 16 Dihedral angle restraints: 10016 sinusoidal: 3861 harmonic: 6155 Sorted by residual: dihedral pdb=" CB CYS C 308 " pdb=" SG CYS C 308 " pdb=" SG CYS C 339 " pdb=" CB CYS C 339 " ideal model delta sinusoidal sigma weight residual -86.00 -173.49 87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS B 74 " pdb=" SG CYS B 74 " pdb=" SG CYS B 105 " pdb=" CB CYS B 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.76 -85.76 1 1.00e+01 1.00e-02 8.89e+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 -149.53 63.53 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 10013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2552 0.161 - 0.322: 15 0.322 - 0.483: 9 0.483 - 0.645: 2 0.645 - 0.806: 1 Chirality restraints: 2579 Sorted by residual: chirality pdb=" CA HIS C 249 " pdb=" N HIS C 249 " pdb=" C HIS C 249 " pdb=" CB HIS C 249 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA PRO B 75 " pdb=" N PRO B 75 " pdb=" C PRO B 75 " pdb=" CB PRO B 75 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA ILE A 359 " pdb=" N ILE A 359 " pdb=" C ILE A 359 " pdb=" CB ILE A 359 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.81e+00 ... (remaining 2576 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 101 " -0.089 2.00e-02 2.50e+03 4.41e-02 4.86e+01 pdb=" CG TRP C 101 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP C 101 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 101 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 101 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 101 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 101 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 101 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 101 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 238 " -0.027 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C ASN C 238 " 0.089 2.00e-02 2.50e+03 pdb=" O ASN C 238 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS C 239 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 99 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ARG C 99 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG C 99 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY C 100 " -0.025 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.73: 7 1.73 - 2.52: 195 2.52 - 3.32: 18690 3.32 - 4.11: 39612 4.11 - 4.90: 74479 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132983 Sorted by model distance: nonbonded pdb=" CD1 LEU A 358 " pdb=" CD2 LEU A 378 " model vdw 0.938 3.880 nonbonded pdb=" CE1 PHE B 463 " pdb=" O SER F 75 " model vdw 1.481 3.340 nonbonded pdb=" OD1 ASP B 220 " pdb=" NH2 ARG F 38 " model vdw 1.541 3.120 nonbonded pdb=" CG LEU A 358 " pdb=" CD2 LEU A 378 " model vdw 1.567 3.890 nonbonded pdb=" CD1 LEU A 358 " pdb=" CG LEU A 378 " model vdw 1.600 3.890 ... (remaining 132978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 150 or resid 161 through 501)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.011 0.558 17026 Z= 0.571 Angle : 1.103 62.075 23084 Z= 0.614 Chirality : 0.060 0.806 2579 Planarity : 0.006 0.090 2912 Dihedral : 13.142 87.633 6037 Min Nonbonded Distance : 0.938 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.02 % Rotamer: Outliers : 2.74 % Allowed : 9.06 % Favored : 88.20 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2154 helix: -1.24 (0.21), residues: 435 sheet: -0.33 (0.19), residues: 727 loop : -3.06 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 73 TYR 0.025 0.002 TYR C 61 PHE 0.013 0.002 PHE D 42 TRP 0.096 0.002 TRP C 101 HIS 0.007 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00832 (17006) covalent geometry : angle 0.89538 (23046) SS BOND : bond 0.19946 ( 19) SS BOND : angle 15.89517 ( 38) hydrogen bonds : bond 0.11616 ( 585) hydrogen bonds : angle 5.99572 ( 1557) Misc. bond : bond 0.03760 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 31 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7793 (ttm170) REVERT: B 386 TYR cc_start: 0.8065 (m-80) cc_final: 0.7782 (m-80) REVERT: B 477 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6875 (mp) REVERT: E 69 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7910 (mp) REVERT: l 34 SER cc_start: 0.8724 (m) cc_final: 0.8500 (t) REVERT: C 151 MET cc_start: 0.6865 (mmm) cc_final: 0.6526 (mmm) outliers start: 49 outliers final: 19 residues processed: 397 average time/residue: 0.1315 time to fit residues: 77.8517 Evaluate side-chains 261 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 494 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 249 HIS A 399 HIS D 7 HIS D 13 GLN L 38 GLN L 39 HIS B 77 GLN B 85 GLN B 103 ASN B 266 HIS B 350 GLN B 446 HIS ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN l 38 GLN l 39 HIS C 134 ASN C 148 HIS C 163 ASN C 249 HIS ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN F 39 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.158298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127308 restraints weight = 19857.956| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17026 Z= 0.160 Angle : 0.668 18.656 23084 Z= 0.348 Chirality : 0.045 0.220 2579 Planarity : 0.005 0.060 2912 Dihedral : 6.665 58.681 2357 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.10 % Favored : 90.76 % Rotamer: Outliers : 3.97 % Allowed : 14.09 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 2154 helix: -0.26 (0.24), residues: 441 sheet: 0.20 (0.20), residues: 694 loop : -2.63 (0.16), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 73 TYR 0.019 0.001 TYR A 61 PHE 0.015 0.001 PHE h 63 TRP 0.035 0.002 TRP B 400 HIS 0.005 0.001 HIS D 7 Details of bonding type rmsd covalent geometry : bond 0.00367 (17006) covalent geometry : angle 0.66578 (23046) SS BOND : bond 0.00533 ( 19) SS BOND : angle 1.45239 ( 38) hydrogen bonds : bond 0.04602 ( 585) hydrogen bonds : angle 5.35573 ( 1557) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 0.588 Fit side-chains REVERT: A 249 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.5394 (p90) REVERT: A 296 ASP cc_start: 0.7754 (p0) cc_final: 0.7476 (p0) REVERT: A 468 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 473 MET cc_start: 0.8353 (mmm) cc_final: 0.7952 (mmt) REVERT: D 31 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8376 (ttm170) REVERT: L 27 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8607 (p) REVERT: L 27 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7610 (p0) REVERT: B 81 TYR cc_start: 0.8738 (t80) cc_final: 0.8358 (t80) REVERT: B 204 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8681 (tp) REVERT: B 386 TYR cc_start: 0.8517 (m-80) cc_final: 0.8229 (m-80) REVERT: B 473 MET cc_start: 0.7155 (tmm) cc_final: 0.6580 (tpp) REVERT: B 477 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7680 (mp) REVERT: C 66 SER cc_start: 0.8456 (t) cc_final: 0.8095 (m) REVERT: C 151 MET cc_start: 0.8643 (mmm) cc_final: 0.8157 (mmm) REVERT: C 487 MET cc_start: 0.6701 (mmp) cc_final: 0.6443 (mmp) outliers start: 71 outliers final: 41 residues processed: 309 average time/residue: 0.1172 time to fit residues: 56.6947 Evaluate side-chains 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL 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 h residue 25 SER Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 94 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN B 85 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 362 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124663 restraints weight = 20061.889| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.08 r_work: 0.3124 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17026 Z= 0.200 Angle : 0.661 18.901 23084 Z= 0.346 Chirality : 0.045 0.206 2579 Planarity : 0.005 0.137 2912 Dihedral : 6.406 57.883 2345 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.54 % Favored : 91.36 % Rotamer: Outliers : 3.86 % Allowed : 16.72 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2154 helix: 0.06 (0.24), residues: 437 sheet: 0.21 (0.20), residues: 729 loop : -2.50 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 2 TYR 0.017 0.001 TYR h 100J PHE 0.015 0.001 PHE E 42 TRP 0.021 0.001 TRP B 400 HIS 0.011 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00467 (17006) covalent geometry : angle 0.66052 (23046) SS BOND : bond 0.00441 ( 19) SS BOND : angle 1.09682 ( 38) hydrogen bonds : bond 0.04667 ( 585) hydrogen bonds : angle 5.23952 ( 1557) Misc. bond : bond 0.00671 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 197 ASP cc_start: 0.8186 (t70) cc_final: 0.7948 (p0) REVERT: A 244 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: A 249 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.5466 (p90) REVERT: A 468 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 473 MET cc_start: 0.8491 (mmm) cc_final: 0.8077 (mmt) REVERT: D 31 ARG cc_start: 0.8696 (ttp-170) cc_final: 0.8391 (ttm170) REVERT: L 27 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7681 (p0) REVERT: B 81 TYR cc_start: 0.8756 (t80) cc_final: 0.8402 (t80) REVERT: B 147 GLN cc_start: 0.8418 (mt0) cc_final: 0.8213 (mt0) REVERT: B 204 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8704 (tp) REVERT: C 151 MET cc_start: 0.8618 (mmm) cc_final: 0.8102 (mmm) outliers start: 69 outliers final: 50 residues processed: 277 average time/residue: 0.1091 time to fit residues: 48.2529 Evaluate side-chains 274 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain h residue 17 SER Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 138 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 85 GLN ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 103 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123615 restraints weight = 19756.107| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.12 r_work: 0.3080 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17026 Z= 0.211 Angle : 0.657 19.343 23084 Z= 0.343 Chirality : 0.045 0.209 2579 Planarity : 0.005 0.119 2912 Dihedral : 6.175 57.826 2341 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.71 % Rotamer: Outliers : 5.54 % Allowed : 16.72 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2154 helix: 0.13 (0.24), residues: 440 sheet: 0.29 (0.20), residues: 717 loop : -2.44 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 2 TYR 0.018 0.002 TYR h 100J PHE 0.015 0.001 PHE E 42 TRP 0.018 0.002 TRP B 400 HIS 0.013 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00496 (17006) covalent geometry : angle 0.65626 (23046) SS BOND : bond 0.00421 ( 19) SS BOND : angle 1.04296 ( 38) hydrogen bonds : bond 0.04698 ( 585) hydrogen bonds : angle 5.17574 ( 1557) Misc. bond : bond 0.00465 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 219 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 249 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.5615 (p90) REVERT: A 296 ASP cc_start: 0.7670 (p0) cc_final: 0.7396 (p0) REVERT: A 468 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 473 MET cc_start: 0.8478 (mmm) cc_final: 0.8098 (mmt) REVERT: D 25 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6383 (p90) REVERT: D 31 ARG cc_start: 0.8731 (ttp-170) cc_final: 0.8449 (ttm170) REVERT: L 27 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8651 (p) REVERT: L 27 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7679 (p0) REVERT: B 79 GLU cc_start: 0.4018 (OUTLIER) cc_final: 0.2496 (mp0) REVERT: B 81 TYR cc_start: 0.8770 (t80) cc_final: 0.8450 (t80) REVERT: B 204 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8768 (tp) REVERT: B 386 TYR cc_start: 0.8653 (m-80) cc_final: 0.8422 (m-80) REVERT: B 448 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8942 (mm) REVERT: B 473 MET cc_start: 0.7180 (tmm) cc_final: 0.6751 (mtt) REVERT: h 71 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7628 (pmt170) REVERT: C 151 MET cc_start: 0.8571 (mmm) cc_final: 0.7991 (mmm) REVERT: C 197 ASP cc_start: 0.8273 (t0) cc_final: 0.7945 (t0) REVERT: C 473 MET cc_start: 0.7842 (mmt) cc_final: 0.7250 (mmt) outliers start: 99 outliers final: 68 residues processed: 288 average time/residue: 0.1123 time to fit residues: 50.6549 Evaluate side-chains 287 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 59 optimal weight: 30.0000 chunk 49 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 447 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.156014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125176 restraints weight = 19868.945| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.12 r_work: 0.3113 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17026 Z= 0.158 Angle : 0.610 17.370 23084 Z= 0.320 Chirality : 0.044 0.235 2579 Planarity : 0.006 0.188 2912 Dihedral : 5.988 58.057 2341 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 5.15 % Allowed : 17.79 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2154 helix: 0.30 (0.25), residues: 439 sheet: 0.39 (0.20), residues: 709 loop : -2.34 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG B 2 TYR 0.016 0.001 TYR A 61 PHE 0.015 0.001 PHE E 42 TRP 0.015 0.001 TRP h 100D HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00363 (17006) covalent geometry : angle 0.60991 (23046) SS BOND : bond 0.00349 ( 19) SS BOND : angle 0.76932 ( 38) hydrogen bonds : bond 0.04302 ( 585) hydrogen bonds : angle 5.07069 ( 1557) Misc. bond : bond 0.00825 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 218 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: A 249 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.5634 (p90) REVERT: A 296 ASP cc_start: 0.7647 (p0) cc_final: 0.7396 (p0) REVERT: A 454 LYS cc_start: 0.8694 (tttt) cc_final: 0.8415 (tttp) REVERT: A 468 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 473 MET cc_start: 0.8451 (mmm) cc_final: 0.8071 (mmt) REVERT: D 25 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6240 (p90) REVERT: D 31 ARG cc_start: 0.8699 (ttp-170) cc_final: 0.8421 (ttm170) REVERT: H 100 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (p) REVERT: L 27 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8638 (p) REVERT: L 27 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7679 (p0) REVERT: B 81 TYR cc_start: 0.8762 (t80) cc_final: 0.8460 (t80) REVERT: B 204 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8781 (tp) REVERT: h 71 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7628 (pmt170) REVERT: C 151 MET cc_start: 0.8581 (mmm) cc_final: 0.8003 (mmm) outliers start: 92 outliers final: 68 residues processed: 285 average time/residue: 0.1106 time to fit residues: 49.8804 Evaluate side-chains 279 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 202 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 491 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 62 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.154327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123046 restraints weight = 19814.238| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.17 r_work: 0.3065 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17026 Z= 0.194 Angle : 0.632 18.609 23084 Z= 0.332 Chirality : 0.045 0.224 2579 Planarity : 0.005 0.175 2912 Dihedral : 5.965 56.966 2339 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.24 % Favored : 90.67 % Rotamer: Outliers : 5.65 % Allowed : 17.56 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2154 helix: 0.38 (0.25), residues: 435 sheet: 0.29 (0.20), residues: 725 loop : -2.33 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 2 TYR 0.016 0.001 TYR h 100J PHE 0.015 0.001 PHE E 42 TRP 0.017 0.001 TRP h 100D HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00454 (17006) covalent geometry : angle 0.63170 (23046) SS BOND : bond 0.00396 ( 19) SS BOND : angle 0.88024 ( 38) hydrogen bonds : bond 0.04441 ( 585) hydrogen bonds : angle 5.09603 ( 1557) Misc. bond : bond 0.00608 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 211 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: A 249 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.5335 (p90) REVERT: A 296 ASP cc_start: 0.7649 (p0) cc_final: 0.7370 (p0) REVERT: A 454 LYS cc_start: 0.8718 (tttt) cc_final: 0.8434 (tttp) REVERT: A 468 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 473 MET cc_start: 0.8390 (mmm) cc_final: 0.8083 (mmt) REVERT: D 25 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.5902 (p90) REVERT: D 31 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8433 (ttm170) REVERT: H 100 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8450 (p) REVERT: L 27 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8593 (p) REVERT: L 27 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7572 (p0) REVERT: B 79 GLU cc_start: 0.3903 (OUTLIER) cc_final: 0.3104 (mp0) REVERT: B 81 TYR cc_start: 0.8711 (t80) cc_final: 0.8387 (t80) REVERT: B 204 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8777 (tp) REVERT: B 386 TYR cc_start: 0.8662 (m-80) cc_final: 0.8419 (m-80) REVERT: B 491 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7119 (tp) REVERT: h 48 MET cc_start: 0.8763 (mtp) cc_final: 0.8425 (mtm) REVERT: h 71 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7635 (pmt170) REVERT: C 151 MET cc_start: 0.8592 (mmm) cc_final: 0.7982 (mmm) REVERT: C 197 ASP cc_start: 0.8277 (t0) cc_final: 0.7876 (t0) REVERT: C 426 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (m-30) outliers start: 101 outliers final: 74 residues processed: 285 average time/residue: 0.1057 time to fit residues: 48.2918 Evaluate side-chains 288 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 202 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 22 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 11 optimal weight: 0.0020 chunk 209 optimal weight: 6.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.152340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120760 restraints weight = 19674.483| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.15 r_work: 0.3011 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17026 Z= 0.243 Angle : 0.677 20.003 23084 Z= 0.354 Chirality : 0.046 0.237 2579 Planarity : 0.006 0.160 2912 Dihedral : 6.097 56.547 2337 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.38 % Favored : 90.48 % Rotamer: Outliers : 5.54 % Allowed : 18.40 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2154 helix: 0.30 (0.25), residues: 435 sheet: 0.19 (0.20), residues: 725 loop : -2.34 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 2 TYR 0.018 0.002 TYR h 100J PHE 0.013 0.001 PHE E 42 TRP 0.018 0.002 TRP h 100D HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00574 (17006) covalent geometry : angle 0.67579 (23046) SS BOND : bond 0.00469 ( 19) SS BOND : angle 1.02155 ( 38) hydrogen bonds : bond 0.04755 ( 585) hydrogen bonds : angle 5.16373 ( 1557) Misc. bond : bond 0.00538 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 213 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 244 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: A 249 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.5347 (p90) REVERT: A 405 SER cc_start: 0.8743 (p) cc_final: 0.8543 (t) REVERT: A 454 LYS cc_start: 0.8741 (tttt) cc_final: 0.8451 (tttp) REVERT: A 468 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 473 MET cc_start: 0.8464 (mmm) cc_final: 0.8239 (mmt) REVERT: D 25 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5896 (p90) REVERT: D 31 ARG cc_start: 0.8730 (ttp-170) cc_final: 0.8446 (ttm170) REVERT: H 100 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (p) REVERT: L 27 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8607 (p) REVERT: L 27 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 79 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.2967 (mp0) REVERT: B 81 TYR cc_start: 0.8735 (t80) cc_final: 0.8406 (t80) REVERT: B 204 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8781 (tp) REVERT: B 251 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7632 (ptmm) REVERT: B 386 TYR cc_start: 0.8672 (m-80) cc_final: 0.8398 (m-80) REVERT: B 460 MET cc_start: 0.8865 (mtm) cc_final: 0.8582 (mtp) REVERT: B 491 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7137 (tp) REVERT: h 28 THR cc_start: 0.8288 (m) cc_final: 0.7629 (p) REVERT: h 71 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7567 (pmt170) REVERT: C 151 MET cc_start: 0.8610 (mmm) cc_final: 0.8204 (mmm) REVERT: C 197 ASP cc_start: 0.8361 (t0) cc_final: 0.7905 (t0) REVERT: C 426 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7806 (m-30) outliers start: 99 outliers final: 73 residues processed: 292 average time/residue: 0.1131 time to fit residues: 51.9077 Evaluate side-chains 292 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 207 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 48 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 159 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS ** C 447 GLN ** 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 = 0.3762 r_free = 0.3762 target = 0.160593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129698 restraints weight = 19800.805| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.16 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17026 Z= 0.109 Angle : 0.565 12.940 23084 Z= 0.299 Chirality : 0.042 0.187 2579 Planarity : 0.005 0.203 2912 Dihedral : 5.569 59.658 2337 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.39 % Rotamer: Outliers : 3.97 % Allowed : 20.19 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2154 helix: 0.65 (0.25), residues: 424 sheet: 0.55 (0.21), residues: 689 loop : -2.21 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 2 TYR 0.017 0.001 TYR A 61 PHE 0.017 0.001 PHE D 42 TRP 0.014 0.001 TRP F 19 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00228 (17006) covalent geometry : angle 0.56547 (23046) SS BOND : bond 0.00203 ( 19) SS BOND : angle 0.50899 ( 38) hydrogen bonds : bond 0.03718 ( 585) hydrogen bonds : angle 4.98345 ( 1557) Misc. bond : bond 0.00668 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: A 249 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.5764 (p90) REVERT: A 454 LYS cc_start: 0.8680 (tttt) cc_final: 0.8467 (tttp) REVERT: A 473 MET cc_start: 0.8320 (mmm) cc_final: 0.7928 (mmt) REVERT: A 487 MET cc_start: 0.6240 (mmp) cc_final: 0.6009 (mmp) REVERT: D 25 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5644 (p90) REVERT: D 31 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8357 (ttm170) REVERT: L 27 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8648 (p) REVERT: L 27 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7816 (p0) REVERT: B 81 TYR cc_start: 0.8772 (t80) cc_final: 0.8401 (t80) REVERT: B 204 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8843 (tp) REVERT: B 491 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7129 (tp) REVERT: h 48 MET cc_start: 0.8798 (mtp) cc_final: 0.8491 (mtm) REVERT: C 151 MET cc_start: 0.8593 (mmm) cc_final: 0.8051 (mmm) REVERT: C 197 ASP cc_start: 0.8401 (t0) cc_final: 0.8052 (t0) REVERT: C 477 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8212 (mp) outliers start: 71 outliers final: 46 residues processed: 284 average time/residue: 0.1138 time to fit residues: 50.4414 Evaluate side-chains 258 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 0.0570 chunk 148 optimal weight: 10.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 401 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127786 restraints weight = 19733.575| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17026 Z= 0.119 Angle : 0.563 14.064 23084 Z= 0.298 Chirality : 0.042 0.182 2579 Planarity : 0.006 0.205 2912 Dihedral : 5.332 59.733 2332 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 3.30 % Allowed : 20.64 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 2154 helix: 0.70 (0.26), residues: 436 sheet: 0.70 (0.21), residues: 672 loop : -2.18 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 2 TYR 0.014 0.001 TYR A 61 PHE 0.018 0.001 PHE E 42 TRP 0.016 0.001 TRP C 474 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00267 (17006) covalent geometry : angle 0.56318 (23046) SS BOND : bond 0.00252 ( 19) SS BOND : angle 0.55957 ( 38) hydrogen bonds : bond 0.03790 ( 585) hydrogen bonds : angle 4.90301 ( 1557) Misc. bond : bond 0.00562 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: A 249 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.5322 (p90) REVERT: A 454 LYS cc_start: 0.8701 (tttt) cc_final: 0.8498 (tttp) REVERT: A 473 MET cc_start: 0.8269 (mmm) cc_final: 0.7875 (mmt) REVERT: D 25 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5614 (p90) REVERT: D 31 ARG cc_start: 0.8646 (ttp-170) cc_final: 0.8425 (ttm170) REVERT: L 27 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8627 (p) REVERT: L 27 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7819 (p0) REVERT: B 15 MET cc_start: 0.6374 (ttp) cc_final: 0.6141 (ttp) REVERT: B 81 TYR cc_start: 0.8751 (t80) cc_final: 0.8470 (t80) REVERT: B 204 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8842 (tp) REVERT: B 251 LYS cc_start: 0.7927 (ptmm) cc_final: 0.7621 (ptmm) REVERT: B 315 THR cc_start: 0.8841 (m) cc_final: 0.8525 (m) REVERT: B 491 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7217 (tp) REVERT: h 28 THR cc_start: 0.8488 (m) cc_final: 0.7791 (p) REVERT: h 48 MET cc_start: 0.8809 (mtp) cc_final: 0.8497 (mtm) REVERT: h 94 ARG cc_start: 0.8589 (ptt180) cc_final: 0.8347 (ptt-90) REVERT: C 151 MET cc_start: 0.8570 (mmm) cc_final: 0.8003 (mmm) REVERT: C 197 ASP cc_start: 0.8375 (t0) cc_final: 0.7935 (t0) REVERT: C 477 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 59 outliers final: 48 residues processed: 264 average time/residue: 0.1017 time to fit residues: 43.1790 Evaluate side-chains 270 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 173 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 201 optimal weight: 0.2980 chunk 144 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 HIS B 371 ASN C 158 HIS C 401 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132370 restraints weight = 19670.994| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.07 r_work: 0.3260 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17026 Z= 0.096 Angle : 0.535 11.175 23084 Z= 0.284 Chirality : 0.041 0.167 2579 Planarity : 0.005 0.178 2912 Dihedral : 5.079 56.674 2332 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 2.85 % Allowed : 21.31 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2154 helix: 1.02 (0.26), residues: 424 sheet: 0.87 (0.21), residues: 663 loop : -2.11 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 2 TYR 0.013 0.001 TYR A 61 PHE 0.017 0.001 PHE E 42 TRP 0.018 0.001 TRP C 474 HIS 0.003 0.001 HIS B 398 Details of bonding type rmsd covalent geometry : bond 0.00202 (17006) covalent geometry : angle 0.53522 (23046) SS BOND : bond 0.00194 ( 19) SS BOND : angle 0.43929 ( 38) hydrogen bonds : bond 0.03413 ( 585) hydrogen bonds : angle 4.79844 ( 1557) Misc. bond : bond 0.00468 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: A 249 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.5697 (p90) REVERT: A 251 LYS cc_start: 0.8976 (ptmt) cc_final: 0.8599 (ttpt) REVERT: D 37 PHE cc_start: 0.8990 (t80) cc_final: 0.8723 (t80) REVERT: L 27 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8623 (p) REVERT: L 27 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7712 (p0) REVERT: B 81 TYR cc_start: 0.8657 (t80) cc_final: 0.8317 (t80) REVERT: B 204 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 473 MET cc_start: 0.7051 (tmm) cc_final: 0.6751 (mtt) REVERT: h 28 THR cc_start: 0.8449 (m) cc_final: 0.7732 (p) REVERT: h 48 MET cc_start: 0.8777 (mtp) cc_final: 0.8474 (mtm) REVERT: C 57 ARG cc_start: 0.8347 (ttm170) cc_final: 0.8035 (ttt180) REVERT: C 151 MET cc_start: 0.8546 (mmm) cc_final: 0.7973 (mmm) REVERT: C 197 ASP cc_start: 0.8287 (t0) cc_final: 0.7836 (t0) REVERT: C 297 LYS cc_start: 0.8442 (mttt) cc_final: 0.8177 (mtmm) REVERT: C 454 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8331 (tttm) REVERT: C 477 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8317 (mp) outliers start: 51 outliers final: 39 residues processed: 286 average time/residue: 0.1087 time to fit residues: 49.3572 Evaluate side-chains 279 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** C 447 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.152552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121224 restraints weight = 19706.970| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3023 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17026 Z= 0.269 Angle : 0.699 19.427 23084 Z= 0.365 Chirality : 0.047 0.208 2579 Planarity : 0.006 0.229 2912 Dihedral : 5.752 59.411 2331 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.87 % Favored : 90.99 % Rotamer: Outliers : 3.02 % Allowed : 21.87 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 2154 helix: 0.50 (0.25), residues: 443 sheet: 0.62 (0.20), residues: 680 loop : -2.31 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG B 2 TYR 0.019 0.002 TYR A 61 PHE 0.015 0.002 PHE C 431 TRP 0.018 0.002 TRP A 101 HIS 0.011 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00638 (17006) covalent geometry : angle 0.69800 (23046) SS BOND : bond 0.00464 ( 19) SS BOND : angle 1.07835 ( 38) hydrogen bonds : bond 0.04649 ( 585) hydrogen bonds : angle 5.10633 ( 1557) Misc. bond : bond 0.00695 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.62 seconds wall clock time: 78 minutes 9.36 seconds (4689.36 seconds total)