Starting phenix.real_space_refine on Sun Jun 8 00:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1r_41825/06_2025/8u1r_41825_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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 60 5.16 5 C 5763 2.51 5 N 1524 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Chain: "B" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Chain: "C" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3042 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain breaks: 1 Time building chain proxies: 5.49, per 1000 atoms: 0.60 Number of scatterers: 9126 At special positions: 0 Unit cell: (100.58, 102.46, 94, 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 60 16.00 O 1779 8.00 N 1524 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 109 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.01 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 109 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 41.4% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 67 through 99 removed outlier: 3.559A pdb=" N ASP A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 4.146A pdb=" N CYS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.552A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.699A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.804A pdb=" N ARG B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 98 Proline residue: B 84 - end of helix removed outlier: 3.585A pdb=" N VAL B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 142 removed outlier: 4.468A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 209 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.309A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.794A pdb=" N ARG C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 99 removed outlier: 3.539A pdb=" N ASP C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 4.056A pdb=" N ASN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 96 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.557A pdb=" N GLY C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'C' and resid 120 through 142 removed outlier: 4.522A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 186 through 209 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 248 through 254 removed outlier: 4.146A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 354 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157 removed outlier: 8.055A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 35 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET A 292 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 37 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.351A pdb=" N GLY A 259 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A 276 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 279 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 46 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR A 281 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS A 44 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.769A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 removed outlier: 4.392A pdb=" N ALA A 359 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407 removed outlier: 3.871A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.710A pdb=" N MET C 110 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 157 removed outlier: 8.054A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.911A pdb=" N ARG B 258 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 279 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER B 46 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR B 281 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS B 44 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS B 35 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N MET B 292 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 37 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.800A pdb=" N MET B 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.802A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 407 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298 removed outlier: 4.589A pdb=" N ALA B 359 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 157 removed outlier: 8.159A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 4.108A pdb=" N ARG C 258 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 279 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER C 46 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR C 281 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS C 44 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 removed outlier: 4.486A pdb=" N ALA C 359 " --> pdb=" O LEU C 306 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1269 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: 2.71 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2994 1.34 - 1.46: 1468 1.46 - 1.58: 4697 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 9243 Sorted by residual: bond pdb=" N ILE C 422 " pdb=" CA ILE C 422 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.23e+01 bond pdb=" N ILE B 422 " pdb=" CA ILE B 422 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N ILE B 420 " pdb=" CA ILE B 420 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.06e+01 bond pdb=" CA SER A 423 " pdb=" CB SER A 423 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.61e-02 3.86e+03 9.07e+00 bond pdb=" N VAL B 96 " pdb=" CA VAL B 96 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.28e-02 6.10e+03 8.91e+00 ... (remaining 9238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12180 2.04 - 4.09: 344 4.09 - 6.13: 39 6.13 - 8.18: 5 8.18 - 10.22: 2 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C CYS A 387 " pdb=" N ARG A 388 " pdb=" CA ARG A 388 " ideal model delta sigma weight residual 122.36 116.09 6.27 1.60e+00 3.91e-01 1.54e+01 angle pdb=" CA SER A 423 " pdb=" C SER A 423 " pdb=" O SER A 423 " ideal model delta sigma weight residual 121.94 117.66 4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" N MET A 390 " pdb=" CA MET A 390 " pdb=" C MET A 390 " ideal model delta sigma weight residual 112.38 107.89 4.49 1.22e+00 6.72e-01 1.36e+01 angle pdb=" CA ILE C 422 " pdb=" C ILE C 422 " pdb=" O ILE C 422 " ideal model delta sigma weight residual 121.67 117.85 3.82 1.05e+00 9.07e-01 1.32e+01 angle pdb=" N VAL A 31 " pdb=" CA VAL A 31 " pdb=" C VAL A 31 " ideal model delta sigma weight residual 113.39 108.07 5.32 1.47e+00 4.63e-01 1.31e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5101 17.85 - 35.71: 450 35.71 - 53.56: 114 53.56 - 71.41: 19 71.41 - 89.26: 19 Dihedral angle restraints: 5703 sinusoidal: 2214 harmonic: 3489 Sorted by residual: dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -170.97 84.97 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -124.15 38.15 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual -86.00 -123.93 37.93 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 5700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1213 0.053 - 0.107: 263 0.107 - 0.160: 67 0.160 - 0.214: 14 0.214 - 0.267: 3 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA ILE A 422 " pdb=" N ILE A 422 " pdb=" C ILE A 422 " pdb=" CB ILE A 422 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE C 422 " pdb=" N ILE C 422 " pdb=" C ILE C 422 " pdb=" CB ILE C 422 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1557 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 90 " 0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C ASN A 90 " -0.099 2.00e-02 2.50e+03 pdb=" O ASN A 90 " 0.037 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 419 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" CG ASP A 419 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 419 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 419 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 57 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO A 58 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.025 5.00e-02 4.00e+02 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 401 2.73 - 3.27: 9226 3.27 - 3.81: 14383 3.81 - 4.36: 17385 4.36 - 4.90: 29620 Nonbonded interactions: 71015 Sorted by model distance: nonbonded pdb=" OH TYR C 41 " pdb=" O ASP C 338 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O ASP B 338 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" O ASP A 338 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR C 329 " pdb=" O SER C 332 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP A 338 " pdb=" OG SER B 365 " model vdw 2.330 3.040 ... (remaining 71010 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.240 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.880 Find NCS groups from input model: 0.280 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.005 0.048 9261 Z= 0.275 Angle : 0.775 10.223 12606 Z= 0.471 Chirality : 0.051 0.267 1560 Planarity : 0.004 0.057 1596 Dihedral : 15.163 89.263 3399 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.05 % Allowed : 13.75 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1185 helix: 0.62 (0.25), residues: 417 sheet: 0.14 (0.31), residues: 252 loop : -0.97 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 303 HIS 0.005 0.001 HIS A 130 PHE 0.012 0.001 PHE B 234 TYR 0.017 0.002 TYR C 415 ARG 0.013 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.20661 ( 459) hydrogen bonds : angle 7.56304 ( 1269) SS BOND : bond 0.00543 ( 18) SS BOND : angle 1.01663 ( 36) covalent geometry : bond 0.00453 ( 9243) covalent geometry : angle 0.77448 (12570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.8080 (mmp) cc_final: 0.7742 (ttt) REVERT: A 399 SER cc_start: 0.6967 (m) cc_final: 0.6452 (p) REVERT: B 390 MET cc_start: 0.7562 (mmp) cc_final: 0.6877 (ttp) REVERT: C 390 MET cc_start: 0.7399 (mmp) cc_final: 0.6865 (ttp) REVERT: C 399 SER cc_start: 0.6770 (m) cc_final: 0.6222 (p) outliers start: 11 outliers final: 3 residues processed: 141 average time/residue: 0.2249 time to fit residues: 43.5072 Evaluate side-chains 123 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN B 384 ASN C 157 GLN C 381 ASN C 384 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110961 restraints weight = 11448.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113676 restraints weight = 7413.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115635 restraints weight = 5400.111| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9261 Z= 0.198 Angle : 0.609 10.584 12606 Z= 0.318 Chirality : 0.045 0.168 1560 Planarity : 0.004 0.035 1596 Dihedral : 5.406 57.316 1282 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.62 % Allowed : 14.33 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1185 helix: 1.16 (0.26), residues: 411 sheet: 0.10 (0.28), residues: 285 loop : -0.88 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 303 HIS 0.006 0.002 HIS C 130 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.002 TYR A 415 ARG 0.006 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 459) hydrogen bonds : angle 5.49537 ( 1269) SS BOND : bond 0.00185 ( 18) SS BOND : angle 0.66140 ( 36) covalent geometry : bond 0.00477 ( 9243) covalent geometry : angle 0.60846 (12570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 TYR cc_start: 0.7290 (t80) cc_final: 0.6956 (t80) REVERT: B 390 MET cc_start: 0.7698 (mmp) cc_final: 0.7064 (ttt) REVERT: C 325 ARG cc_start: 0.8248 (mtm110) cc_final: 0.8032 (mtm180) REVERT: C 390 MET cc_start: 0.7368 (mmp) cc_final: 0.6783 (ttt) REVERT: C 399 SER cc_start: 0.7099 (m) cc_final: 0.6743 (p) outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 0.2097 time to fit residues: 40.3925 Evaluate side-chains 114 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 88 optimal weight: 2.9990 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117874 restraints weight = 11362.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120388 restraints weight = 7373.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122374 restraints weight = 5424.391| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9261 Z= 0.120 Angle : 0.534 8.030 12606 Z= 0.280 Chirality : 0.043 0.160 1560 Planarity : 0.003 0.032 1596 Dihedral : 4.761 30.400 1276 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 13.94 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1185 helix: 1.47 (0.26), residues: 414 sheet: 0.10 (0.29), residues: 285 loop : -0.78 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.015 0.001 PHE C 234 TYR 0.009 0.001 TYR A 296 ARG 0.006 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 459) hydrogen bonds : angle 5.04019 ( 1269) SS BOND : bond 0.00364 ( 18) SS BOND : angle 0.87953 ( 36) covalent geometry : bond 0.00272 ( 9243) covalent geometry : angle 0.53266 (12570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.102 Fit side-chains REVERT: B 390 MET cc_start: 0.7779 (mmp) cc_final: 0.7193 (ttt) REVERT: C 390 MET cc_start: 0.7333 (mmp) cc_final: 0.6678 (ttt) outliers start: 27 outliers final: 16 residues processed: 136 average time/residue: 0.1787 time to fit residues: 36.2383 Evaluate side-chains 120 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 42 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN C 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120197 restraints weight = 11116.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123151 restraints weight = 6987.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125207 restraints weight = 4988.691| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9261 Z= 0.103 Angle : 0.503 6.705 12606 Z= 0.264 Chirality : 0.043 0.155 1560 Planarity : 0.003 0.036 1596 Dihedral : 4.548 30.990 1276 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.77 % Allowed : 13.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1185 helix: 1.51 (0.26), residues: 432 sheet: 0.10 (0.29), residues: 285 loop : -0.52 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.005 0.001 HIS C 253 PHE 0.014 0.001 PHE B 234 TYR 0.009 0.001 TYR C 415 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 459) hydrogen bonds : angle 4.74758 ( 1269) SS BOND : bond 0.00162 ( 18) SS BOND : angle 0.68808 ( 36) covalent geometry : bond 0.00227 ( 9243) covalent geometry : angle 0.50252 (12570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.825 Fit side-chains REVERT: A 420 ILE cc_start: 0.8545 (tt) cc_final: 0.8326 (pt) REVERT: B 390 MET cc_start: 0.7868 (mmp) cc_final: 0.7137 (ttt) REVERT: C 390 MET cc_start: 0.7376 (mmp) cc_final: 0.6566 (ttt) outliers start: 29 outliers final: 13 residues processed: 138 average time/residue: 0.1907 time to fit residues: 40.8386 Evaluate side-chains 116 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 0.0020 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.104150 restraints weight = 11442.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106598 restraints weight = 7687.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108423 restraints weight = 5710.632| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9261 Z= 0.109 Angle : 0.508 6.765 12606 Z= 0.263 Chirality : 0.043 0.168 1560 Planarity : 0.003 0.036 1596 Dihedral : 4.355 22.320 1275 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.67 % Allowed : 14.52 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1185 helix: 1.55 (0.26), residues: 432 sheet: -0.07 (0.29), residues: 270 loop : -0.29 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.014 0.001 PHE B 234 TYR 0.009 0.001 TYR A 270 ARG 0.004 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 459) hydrogen bonds : angle 4.62622 ( 1269) SS BOND : bond 0.00149 ( 18) SS BOND : angle 0.65124 ( 36) covalent geometry : bond 0.00247 ( 9243) covalent geometry : angle 0.50751 (12570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.954 Fit side-chains REVERT: B 390 MET cc_start: 0.7821 (mmp) cc_final: 0.7149 (ttt) REVERT: C 390 MET cc_start: 0.7387 (mmp) cc_final: 0.6627 (ttt) outliers start: 28 outliers final: 17 residues processed: 132 average time/residue: 0.1338 time to fit residues: 28.2616 Evaluate side-chains 129 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 408 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105150 restraints weight = 11397.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107607 restraints weight = 7564.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109441 restraints weight = 5630.473| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9261 Z= 0.103 Angle : 0.509 8.457 12606 Z= 0.262 Chirality : 0.043 0.161 1560 Planarity : 0.003 0.039 1596 Dihedral : 4.273 22.318 1275 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 15.57 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1185 helix: 1.64 (0.26), residues: 432 sheet: -0.07 (0.29), residues: 270 loop : -0.28 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.013 0.001 PHE B 234 TYR 0.018 0.001 TYR B 379 ARG 0.005 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 459) hydrogen bonds : angle 4.52692 ( 1269) SS BOND : bond 0.00147 ( 18) SS BOND : angle 0.58219 ( 36) covalent geometry : bond 0.00233 ( 9243) covalent geometry : angle 0.50847 (12570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.084 Fit side-chains REVERT: A 60 ILE cc_start: 0.7647 (mm) cc_final: 0.7292 (mm) REVERT: B 390 MET cc_start: 0.7820 (mmp) cc_final: 0.7115 (ttt) REVERT: C 390 MET cc_start: 0.7332 (mmp) cc_final: 0.6545 (ttt) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.1587 time to fit residues: 34.5437 Evaluate side-chains 124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 97 optimal weight: 0.0770 chunk 115 optimal weight: 7.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103317 restraints weight = 11662.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105876 restraints weight = 7841.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.107695 restraints weight = 5836.806| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9261 Z= 0.122 Angle : 0.530 8.937 12606 Z= 0.270 Chirality : 0.043 0.157 1560 Planarity : 0.003 0.036 1596 Dihedral : 4.285 22.449 1275 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.58 % Allowed : 16.14 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1185 helix: 1.67 (0.26), residues: 432 sheet: -0.06 (0.30), residues: 270 loop : -0.27 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.015 0.001 PHE B 234 TYR 0.015 0.001 TYR A 379 ARG 0.004 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 459) hydrogen bonds : angle 4.51161 ( 1269) SS BOND : bond 0.00151 ( 18) SS BOND : angle 0.56243 ( 36) covalent geometry : bond 0.00290 ( 9243) covalent geometry : angle 0.52959 (12570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.185 Fit side-chains REVERT: B 200 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: B 390 MET cc_start: 0.7838 (mmp) cc_final: 0.7109 (ttt) REVERT: C 390 MET cc_start: 0.7341 (mmp) cc_final: 0.6542 (ttt) outliers start: 27 outliers final: 20 residues processed: 132 average time/residue: 0.2409 time to fit residues: 50.2953 Evaluate side-chains 134 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 0.0010 chunk 18 optimal weight: 0.0020 chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 chunk 47 optimal weight: 2.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116157 restraints weight = 11352.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118705 restraints weight = 7326.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120826 restraints weight = 5365.606| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9261 Z= 0.095 Angle : 0.505 8.168 12606 Z= 0.258 Chirality : 0.042 0.159 1560 Planarity : 0.003 0.038 1596 Dihedral : 4.148 21.779 1275 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.29 % Allowed : 16.62 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1185 helix: 1.78 (0.26), residues: 432 sheet: -0.09 (0.32), residues: 240 loop : -0.24 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 303 HIS 0.005 0.001 HIS B 130 PHE 0.014 0.001 PHE B 234 TYR 0.015 0.001 TYR B 379 ARG 0.004 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 459) hydrogen bonds : angle 4.39841 ( 1269) SS BOND : bond 0.00136 ( 18) SS BOND : angle 0.52455 ( 36) covalent geometry : bond 0.00211 ( 9243) covalent geometry : angle 0.50456 (12570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.379 Fit side-chains REVERT: B 200 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 390 MET cc_start: 0.7798 (mmp) cc_final: 0.7051 (ttt) REVERT: C 390 MET cc_start: 0.7205 (mmp) cc_final: 0.6455 (ttt) outliers start: 24 outliers final: 16 residues processed: 132 average time/residue: 0.2282 time to fit residues: 46.5129 Evaluate side-chains 131 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 345 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112366 restraints weight = 11316.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114973 restraints weight = 7432.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116936 restraints weight = 5468.597| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9261 Z= 0.147 Angle : 0.552 8.204 12606 Z= 0.280 Chirality : 0.044 0.172 1560 Planarity : 0.003 0.034 1596 Dihedral : 4.288 21.865 1275 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 16.91 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1185 helix: 1.74 (0.26), residues: 432 sheet: -0.05 (0.30), residues: 270 loop : -0.29 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.015 0.001 PHE C 234 TYR 0.014 0.001 TYR C 415 ARG 0.004 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 459) hydrogen bonds : angle 4.52508 ( 1269) SS BOND : bond 0.00164 ( 18) SS BOND : angle 0.59293 ( 36) covalent geometry : bond 0.00361 ( 9243) covalent geometry : angle 0.55148 (12570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.067 Fit side-chains REVERT: B 200 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: B 390 MET cc_start: 0.7890 (mmp) cc_final: 0.7115 (ttt) REVERT: C 390 MET cc_start: 0.7221 (mmp) cc_final: 0.6410 (ttt) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.1976 time to fit residues: 36.6944 Evaluate side-chains 125 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.4980 chunk 96 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105804 restraints weight = 11558.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108186 restraints weight = 7723.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110135 restraints weight = 5782.839| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9261 Z= 0.104 Angle : 0.524 9.103 12606 Z= 0.264 Chirality : 0.043 0.170 1560 Planarity : 0.003 0.033 1596 Dihedral : 4.197 21.799 1275 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.91 % Allowed : 17.10 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1185 helix: 1.79 (0.26), residues: 432 sheet: -0.11 (0.33), residues: 240 loop : -0.29 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.005 0.001 HIS B 130 PHE 0.015 0.001 PHE B 234 TYR 0.019 0.001 TYR A 427 ARG 0.003 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 459) hydrogen bonds : angle 4.41846 ( 1269) SS BOND : bond 0.00135 ( 18) SS BOND : angle 0.50681 ( 36) covalent geometry : bond 0.00238 ( 9243) covalent geometry : angle 0.52405 (12570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.305 Fit side-chains REVERT: B 200 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 390 MET cc_start: 0.7923 (mmp) cc_final: 0.7073 (ttt) REVERT: C 390 MET cc_start: 0.7239 (mmp) cc_final: 0.6413 (ttt) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.2155 time to fit residues: 42.0728 Evaluate side-chains 126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 87 optimal weight: 0.0770 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119328 restraints weight = 11222.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122090 restraints weight = 7189.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124027 restraints weight = 5185.791| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9261 Z= 0.094 Angle : 0.509 8.826 12606 Z= 0.257 Chirality : 0.042 0.162 1560 Planarity : 0.003 0.034 1596 Dihedral : 4.091 21.383 1275 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.91 % Allowed : 17.00 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1185 helix: 1.90 (0.26), residues: 432 sheet: -0.01 (0.30), residues: 270 loop : -0.19 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.005 0.001 HIS B 130 PHE 0.013 0.001 PHE B 234 TYR 0.018 0.001 TYR A 427 ARG 0.003 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 459) hydrogen bonds : angle 4.32530 ( 1269) SS BOND : bond 0.00112 ( 18) SS BOND : angle 0.53256 ( 36) covalent geometry : bond 0.00206 ( 9243) covalent geometry : angle 0.50920 (12570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.47 seconds wall clock time: 60 minutes 12.10 seconds (3612.10 seconds total)