Starting phenix.real_space_refine on Thu Jul 2 16:02:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxs_36711/07_2026/8jxs_36711.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 871 atoms to isotropic. 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 41 5.16 5 C 5539 2.51 5 N 1422 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8596 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 929 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2649 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1536 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'V6X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8596 At special positions: 0 Unit cell: (133.488, 123.6, 100.528, 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 41 16.00 O 1594 8.00 N 1422 7.00 C 5539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 307 " 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: 0.64 Conformation dependent library (CDL) restraints added in 370.3 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 41.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 22 through 51 removed outlier: 3.775A pdb=" N PHE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 95 through 127 Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.665A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 removed outlier: 3.654A pdb=" N ILE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 203 through 236 Processing helix chain 'A' and resid 265 through 298 removed outlier: 3.992A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.935A pdb=" N PHE A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'C' and resid 43 through 52 Proline residue: C 49 - end of helix Processing helix chain 'C' and resid 65 through 75 removed outlier: 4.568A pdb=" N GLY C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 90 removed outlier: 3.534A pdb=" N LYS C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 90 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.758A pdb=" N TRP C 95 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.517A pdb=" N LYS C 138 " --> pdb=" O PRO C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 165 removed outlier: 4.150A pdb=" N THR C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Proline residue: C 160 - end of helix removed outlier: 4.357A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 336 through 352 removed outlier: 3.729A pdb=" N TYR C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 370 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.526A pdb=" N GLU C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 518 removed outlier: 3.647A pdb=" N ALA C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.551A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.971A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY L 133 " --> pdb=" O GLN L 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.151A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN B 32 " --> pdb=" O HIS B 52 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS B 52 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.151A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.665A pdb=" N TRP C 63 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 264 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 261 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 111 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 263 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.665A pdb=" N TRP C 63 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 264 " --> pdb=" O TRP C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA9, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.126A pdb=" N VAL C 486 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 493 " --> pdb=" O ASP H 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.042A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.669A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.649A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.503A pdb=" N GLN L 96 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR L 102 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.543A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1287 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: 1.38 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2703 1.35 - 1.46: 2163 1.46 - 1.58: 3877 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 8805 Sorted by residual: bond pdb=" C09 V6X A 401 " pdb=" N13 V6X A 401 " ideal model delta sigma weight residual 1.379 1.302 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C03 V6X A 401 " pdb=" C04 V6X A 401 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C18 V6X A 401 " pdb=" O17 V6X A 401 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" C25 V6X A 401 " pdb=" O26 V6X A 401 " ideal model delta sigma weight residual 1.364 1.307 0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C24 V6X A 401 " pdb=" C25 V6X A 401 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 8800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11832 1.55 - 3.10: 84 3.10 - 4.66: 53 4.66 - 6.21: 4 6.21 - 7.76: 2 Bond angle restraints: 11975 Sorted by residual: angle pdb=" N VAL B 48 " pdb=" CA VAL B 48 " pdb=" C VAL B 48 " ideal model delta sigma weight residual 111.56 108.77 2.79 8.60e-01 1.35e+00 1.05e+01 angle pdb=" C16 V6X A 401 " pdb=" O17 V6X A 401 " pdb=" C18 V6X A 401 " ideal model delta sigma weight residual 118.59 110.83 7.76 3.00e+00 1.11e-01 6.69e+00 angle pdb=" N SER L 58 " pdb=" CA SER L 58 " pdb=" C SER L 58 " ideal model delta sigma weight residual 114.56 111.35 3.21 1.27e+00 6.20e-01 6.39e+00 angle pdb=" N ALA L 57 " pdb=" CA ALA L 57 " pdb=" CB ALA L 57 " ideal model delta sigma weight residual 113.65 110.32 3.33 1.47e+00 4.63e-01 5.13e+00 angle pdb=" C21 V6X A 401 " pdb=" C22 V6X A 401 " pdb=" O26 V6X A 401 " ideal model delta sigma weight residual 127.45 133.93 -6.48 3.00e+00 1.11e-01 4.67e+00 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 5047 14.56 - 29.11: 99 29.11 - 43.67: 20 43.67 - 58.22: 3 58.22 - 72.78: 2 Dihedral angle restraints: 5171 sinusoidal: 1956 harmonic: 3215 Sorted by residual: dihedral pdb=" CA LEU L 39 " pdb=" CB LEU L 39 " pdb=" CG LEU L 39 " pdb=" CD1 LEU L 39 " ideal model delta sinusoidal sigma weight residual 180.00 137.84 42.16 3 1.50e+01 4.44e-03 7.56e+00 dihedral pdb=" CA ILE A 277 " pdb=" C ILE A 277 " pdb=" N MET A 278 " pdb=" CA MET A 278 " ideal model delta harmonic sigma weight residual -180.00 -166.57 -13.43 0 5.00e+00 4.00e-02 7.22e+00 dihedral pdb=" CA PHE A 203 " pdb=" C PHE A 203 " pdb=" N TYR A 204 " pdb=" CA TYR A 204 " ideal model delta harmonic sigma weight residual -180.00 -167.25 -12.75 0 5.00e+00 4.00e-02 6.51e+00 ... (remaining 5168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 827 0.025 - 0.050: 321 0.050 - 0.075: 97 0.075 - 0.101: 58 0.101 - 0.126: 46 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA ILE L 81 " pdb=" N ILE L 81 " pdb=" C ILE L 81 " pdb=" CB ILE L 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL A 22 " pdb=" N VAL A 22 " pdb=" C VAL A 22 " pdb=" CB VAL A 22 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1346 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO H 159 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 145 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C SER A 145 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 145 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 146 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 205 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 206 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.015 5.00e-02 4.00e+02 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 819 2.74 - 3.28: 8671 3.28 - 3.82: 13932 3.82 - 4.36: 16405 4.36 - 4.90: 29277 Nonbonded interactions: 69104 Sorted by model distance: nonbonded pdb=" O ALA C 343 " pdb=" OG1 THR C 346 " model vdw 2.205 3.040 nonbonded pdb=" O ALA A 101 " pdb=" OG SER A 155 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" N SER A 310 " model vdw 2.281 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.293 3.120 nonbonded pdb=" NE1 TRP A 90 " pdb=" O PHE A 92 " model vdw 2.312 3.120 ... (remaining 69099 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8807 Z= 0.141 Angle : 0.471 7.758 11979 Z= 0.255 Chirality : 0.038 0.126 1349 Planarity : 0.003 0.042 1506 Dihedral : 6.799 72.778 3087 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.23), residues: 1072 helix: -0.44 (0.24), residues: 392 sheet: -0.87 (0.29), residues: 248 loop : -1.28 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.007 0.001 TYR L 97 PHE 0.005 0.001 PHE B 29 TRP 0.003 0.000 TRP A 112 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 8805) covalent geometry : angle 0.47074 / 0.26 (11975) SS BOND : bond 0.00038 / 0.02 ( 2) SS BOND : angle 0.14442 / 0.07 ( 4) hydrogen bonds : bond 0.13237 / 9.59 ( 457) hydrogen bonds : angle 6.13731 / 4.49 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 ASP cc_start: 0.6494 (t0) cc_final: 0.6220 (t70) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.4743 time to fit residues: 136.5999 Evaluate side-chains 148 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS A 224 GLN B 13 GLN C 228 ASN C 350 ASN C 356 GLN C 515 ASN H 13 GLN L 129 GLN L 163 ASN L 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079730 restraints weight = 19864.481| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.16 r_work: 0.3104 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8807 Z= 0.128 Angle : 0.606 8.817 11979 Z= 0.293 Chirality : 0.041 0.152 1349 Planarity : 0.004 0.046 1506 Dihedral : 3.116 14.330 1178 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.16 % Allowed : 13.83 % Favored : 83.01 % 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: 0.23 (0.25), residues: 1072 helix: 1.32 (0.26), residues: 401 sheet: -0.22 (0.29), residues: 261 loop : -0.66 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 233 TYR 0.015 0.001 TYR C 513 PHE 0.014 0.001 PHE C 510 TRP 0.009 0.001 TRP L 101 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8805) covalent geometry : angle 0.60639 / 0.29 (11975) SS BOND : bond 0.00353 / 0.19 ( 2) SS BOND : angle 0.78936 / 0.46 ( 4) hydrogen bonds : bond 0.03220 / 2.28 ( 457) hydrogen bonds : angle 4.43832 / 3.23 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 CYS cc_start: 0.9040 (t) cc_final: 0.8677 (m) REVERT: A 331 TYR cc_start: 0.9029 (m-80) cc_final: 0.8801 (m-80) REVERT: B 46 GLU cc_start: 0.8588 (pt0) cc_final: 0.8370 (pp20) REVERT: C 47 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8326 (tmtt) REVERT: C 112 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7600 (mm-30) REVERT: C 136 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8129 (pp) REVERT: C 181 ASP cc_start: 0.8580 (t0) cc_final: 0.8091 (t70) REVERT: C 317 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8066 (ptp-170) REVERT: C 350 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8175 (m110) REVERT: C 532 PHE cc_start: 0.5757 (m-80) cc_final: 0.5480 (m-10) REVERT: H 46 GLU cc_start: 0.9160 (tt0) cc_final: 0.8774 (pt0) REVERT: H 93 MET cc_start: 0.8590 (tpp) cc_final: 0.8186 (tpp) REVERT: H 209 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7828 (m-40) REVERT: H 211 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8786 (mmmt) REVERT: H 216 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8562 (mmmm) REVERT: L 110 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: L 123 PHE cc_start: 0.7068 (m-10) cc_final: 0.6707 (m-10) outliers start: 29 outliers final: 8 residues processed: 186 average time/residue: 0.4947 time to fit residues: 97.8860 Evaluate side-chains 151 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain L residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.0020 chunk 54 optimal weight: 2.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 44 GLN B 61 ASN B 96 ASN H 13 GLN L 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077771 restraints weight = 19776.612| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.12 r_work: 0.3068 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8807 Z= 0.113 Angle : 0.568 9.893 11979 Z= 0.276 Chirality : 0.041 0.167 1349 Planarity : 0.004 0.045 1506 Dihedral : 3.275 14.268 1178 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.94 % Allowed : 15.90 % Favored : 81.15 % 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: 0.71 (0.25), residues: 1072 helix: 1.72 (0.26), residues: 404 sheet: 0.15 (0.30), residues: 255 loop : -0.51 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.012 0.001 TYR C 107 PHE 0.011 0.001 PHE L 121 TRP 0.008 0.001 TRP A 112 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8805) covalent geometry : angle 0.56816 / 0.28 (11975) SS BOND : bond 0.00260 / 0.14 ( 2) SS BOND : angle 0.33091 / 0.19 ( 4) hydrogen bonds : bond 0.02955 / 2.06 ( 457) hydrogen bonds : angle 4.21500 / 3.07 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 CYS cc_start: 0.9067 (t) cc_final: 0.8578 (m) REVERT: A 165 LYS cc_start: 0.7695 (mmmm) cc_final: 0.7267 (tmtt) REVERT: A 222 GLN cc_start: 0.8874 (tt0) cc_final: 0.8525 (tt0) REVERT: A 267 GLU cc_start: 0.7558 (tt0) cc_final: 0.7172 (tt0) REVERT: A 275 SER cc_start: 0.8445 (t) cc_final: 0.8197 (p) REVERT: B 106 ASP cc_start: 0.8983 (p0) cc_final: 0.8642 (p0) REVERT: C 112 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7612 (mm-30) REVERT: C 136 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8134 (pp) REVERT: C 181 ASP cc_start: 0.8635 (t0) cc_final: 0.8272 (t70) REVERT: C 349 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (mp) REVERT: C 350 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7910 (t0) REVERT: H 93 MET cc_start: 0.8541 (tpp) cc_final: 0.8233 (tpp) REVERT: H 153 LYS cc_start: 0.7562 (tttm) cc_final: 0.7252 (tttp) REVERT: H 211 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8811 (mmmt) REVERT: H 216 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8602 (mmmm) REVERT: L 87 GLU cc_start: 0.9106 (pm20) cc_final: 0.8866 (pm20) outliers start: 27 outliers final: 6 residues processed: 162 average time/residue: 0.5253 time to fit residues: 90.6968 Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 44 GLN B 96 ASN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073708 restraints weight = 20149.648| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.14 r_work: 0.3005 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8807 Z= 0.114 Angle : 0.557 10.255 11979 Z= 0.271 Chirality : 0.041 0.163 1349 Planarity : 0.004 0.041 1506 Dihedral : 3.402 14.407 1178 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.61 % Allowed : 17.32 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1072 helix: 1.97 (0.26), residues: 404 sheet: 0.36 (0.30), residues: 255 loop : -0.33 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 107 TYR 0.015 0.001 TYR C 107 PHE 0.010 0.001 PHE C 93 TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8805) covalent geometry : angle 0.55658 / 0.27 (11975) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.41207 / 0.23 ( 4) hydrogen bonds : bond 0.02925 / 2.02 ( 457) hydrogen bonds : angle 4.12541 / 3.00 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8728 (mm110) cc_final: 0.8314 (tt0) REVERT: A 218 TYR cc_start: 0.8979 (t80) cc_final: 0.8699 (t80) REVERT: A 222 GLN cc_start: 0.8864 (tt0) cc_final: 0.8642 (tt0) REVERT: A 267 GLU cc_start: 0.7798 (tt0) cc_final: 0.6942 (mm-30) REVERT: A 275 SER cc_start: 0.8626 (t) cc_final: 0.8374 (p) REVERT: B 106 ASP cc_start: 0.9072 (p0) cc_final: 0.8757 (p0) REVERT: C 112 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7634 (mm-30) REVERT: C 136 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8243 (pp) REVERT: C 181 ASP cc_start: 0.8669 (t0) cc_final: 0.8212 (t70) REVERT: C 350 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7535 (t0) REVERT: H 76 LYS cc_start: 0.9261 (ptpp) cc_final: 0.8925 (ptpp) REVERT: H 93 MET cc_start: 0.8523 (tpp) cc_final: 0.8237 (tpp) REVERT: H 153 LYS cc_start: 0.7623 (tttm) cc_final: 0.7373 (tttt) REVERT: H 211 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8794 (mmmt) REVERT: H 216 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8638 (mmmm) REVERT: L 87 GLU cc_start: 0.9116 (pm20) cc_final: 0.8777 (pm20) REVERT: L 113 ARG cc_start: 0.8456 (ptm160) cc_final: 0.8000 (ptm-80) REVERT: L 121 PHE cc_start: 0.7850 (m-10) cc_final: 0.7614 (m-10) outliers start: 24 outliers final: 8 residues processed: 159 average time/residue: 0.5660 time to fit residues: 96.0277 Evaluate side-chains 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 224 GLN B 96 ASN C 219 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072390 restraints weight = 19701.812| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.06 r_work: 0.2963 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8807 Z= 0.134 Angle : 0.590 10.961 11979 Z= 0.289 Chirality : 0.041 0.166 1349 Planarity : 0.004 0.065 1506 Dihedral : 3.557 16.861 1178 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.05 % Allowed : 18.41 % Favored : 78.54 % 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: 1.18 (0.26), residues: 1072 helix: 2.04 (0.26), residues: 404 sheet: 0.45 (0.31), residues: 252 loop : -0.18 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 355 TYR 0.018 0.001 TYR B 109 PHE 0.014 0.001 PHE C 364 TRP 0.008 0.001 TRP A 112 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8805) covalent geometry : angle 0.59000 / 0.29 (11975) SS BOND : bond 0.00193 / 0.10 ( 2) SS BOND : angle 0.34569 / 0.19 ( 4) hydrogen bonds : bond 0.03088 / 2.15 ( 457) hydrogen bonds : angle 4.13604 / 3.01 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8720 (mm110) cc_final: 0.8198 (tm-30) REVERT: A 218 TYR cc_start: 0.9052 (t80) cc_final: 0.8763 (t80) REVERT: A 267 GLU cc_start: 0.7852 (tt0) cc_final: 0.7089 (mm-30) REVERT: A 275 SER cc_start: 0.8825 (t) cc_final: 0.8551 (p) REVERT: B 3 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (mm-40) REVERT: B 72 ASP cc_start: 0.7760 (t0) cc_final: 0.7216 (t0) REVERT: B 106 ASP cc_start: 0.9029 (p0) cc_final: 0.8732 (p0) REVERT: C 112 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7651 (mm-30) REVERT: C 181 ASP cc_start: 0.8685 (t0) cc_final: 0.8268 (t70) REVERT: C 350 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8053 (t160) REVERT: C 356 GLN cc_start: 0.7228 (pt0) cc_final: 0.6771 (pt0) REVERT: H 76 LYS cc_start: 0.9206 (ptpp) cc_final: 0.8898 (ptpp) REVERT: H 93 MET cc_start: 0.8583 (tpp) cc_final: 0.8293 (tpp) REVERT: H 108 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: H 153 LYS cc_start: 0.7725 (tttm) cc_final: 0.7474 (tttt) REVERT: H 211 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8771 (mmmt) REVERT: H 216 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8657 (mmmm) REVERT: L 87 GLU cc_start: 0.9149 (pm20) cc_final: 0.8748 (pm20) REVERT: L 121 PHE cc_start: 0.7890 (m-10) cc_final: 0.7635 (m-10) REVERT: L 172 ASP cc_start: 0.7475 (p0) cc_final: 0.7024 (p0) REVERT: L 175 ASP cc_start: 0.8189 (t0) cc_final: 0.7976 (t70) outliers start: 28 outliers final: 11 residues processed: 150 average time/residue: 0.5508 time to fit residues: 88.3305 Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN A 224 GLN B 96 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072440 restraints weight = 19591.917| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.07 r_work: 0.2968 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8807 Z= 0.113 Angle : 0.575 10.891 11979 Z= 0.280 Chirality : 0.041 0.175 1349 Planarity : 0.004 0.039 1506 Dihedral : 3.586 21.737 1178 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.27 % Allowed : 18.85 % Favored : 77.89 % 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: 1.30 (0.26), residues: 1072 helix: 2.17 (0.26), residues: 405 sheet: 0.48 (0.31), residues: 252 loop : -0.13 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.015 0.001 TYR C 107 PHE 0.011 0.001 PHE L 144 TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8805) covalent geometry : angle 0.57477 / 0.28 (11975) SS BOND : bond 0.00128 / 0.07 ( 2) SS BOND : angle 0.50162 / 0.27 ( 4) hydrogen bonds : bond 0.02937 / 2.02 ( 457) hydrogen bonds : angle 4.05768 / 2.95 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8682 (mm110) cc_final: 0.8197 (tm-30) REVERT: A 222 GLN cc_start: 0.8890 (tt0) cc_final: 0.8462 (tp-100) REVERT: A 267 GLU cc_start: 0.7735 (tt0) cc_final: 0.7292 (mm-30) REVERT: B 72 ASP cc_start: 0.7881 (t0) cc_final: 0.7263 (t0) REVERT: B 106 ASP cc_start: 0.9061 (p0) cc_final: 0.8811 (p0) REVERT: C 112 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7711 (mm-30) REVERT: C 181 ASP cc_start: 0.8701 (t0) cc_final: 0.8294 (t70) REVERT: C 350 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.7718 (t0) REVERT: C 356 GLN cc_start: 0.7106 (pt0) cc_final: 0.6735 (pt0) REVERT: H 93 MET cc_start: 0.8563 (tpp) cc_final: 0.8275 (tpp) REVERT: H 153 LYS cc_start: 0.7756 (tttm) cc_final: 0.7487 (tttt) REVERT: H 211 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8773 (mmmt) REVERT: H 216 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (mmmm) REVERT: L 51 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8849 (ptmm) REVERT: L 87 GLU cc_start: 0.9155 (pm20) cc_final: 0.8741 (pm20) REVERT: L 121 PHE cc_start: 0.7943 (m-10) cc_final: 0.7675 (m-10) REVERT: L 172 ASP cc_start: 0.7423 (p0) cc_final: 0.6958 (p0) REVERT: L 175 ASP cc_start: 0.8217 (t0) cc_final: 0.7909 (t0) outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 0.5531 time to fit residues: 89.3642 Evaluate side-chains 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 44 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072275 restraints weight = 19970.971| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.09 r_work: 0.2964 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8807 Z= 0.109 Angle : 0.575 10.779 11979 Z= 0.280 Chirality : 0.041 0.178 1349 Planarity : 0.003 0.030 1506 Dihedral : 3.610 23.567 1178 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.49 % Allowed : 19.28 % Favored : 77.23 % 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: 1.37 (0.26), residues: 1072 helix: 2.22 (0.26), residues: 405 sheet: 0.55 (0.31), residues: 252 loop : -0.10 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 355 TYR 0.013 0.001 TYR C 107 PHE 0.031 0.001 PHE L 144 TRP 0.008 0.001 TRP C 233 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8805) covalent geometry : angle 0.57476 / 0.28 (11975) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.31494 / 0.18 ( 4) hydrogen bonds : bond 0.02911 / 2.00 ( 457) hydrogen bonds : angle 4.02890 / 2.93 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8669 (mm110) cc_final: 0.8184 (tm-30) REVERT: A 222 GLN cc_start: 0.8887 (tt0) cc_final: 0.8460 (tp-100) REVERT: A 267 GLU cc_start: 0.7696 (tt0) cc_final: 0.7284 (mm-30) REVERT: A 275 SER cc_start: 0.8785 (t) cc_final: 0.8584 (p) REVERT: A 339 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8513 (mtmm) REVERT: B 3 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8908 (mm-40) REVERT: B 72 ASP cc_start: 0.7898 (t0) cc_final: 0.7274 (t0) REVERT: B 106 ASP cc_start: 0.9069 (p0) cc_final: 0.8823 (p0) REVERT: C 112 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7691 (mm-30) REVERT: C 350 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8154 (t160) REVERT: C 356 GLN cc_start: 0.7118 (pt0) cc_final: 0.6763 (pt0) REVERT: H 93 MET cc_start: 0.8551 (tpp) cc_final: 0.8255 (tpp) REVERT: H 153 LYS cc_start: 0.7759 (tttm) cc_final: 0.7412 (tttp) REVERT: H 211 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8786 (mmmt) REVERT: H 216 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8632 (mmmm) REVERT: L 51 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8844 (ptmm) REVERT: L 87 GLU cc_start: 0.9155 (pm20) cc_final: 0.8766 (pm20) REVERT: L 121 PHE cc_start: 0.7960 (m-10) cc_final: 0.7693 (m-10) REVERT: L 148 GLU cc_start: 0.8035 (pm20) cc_final: 0.7542 (pm20) REVERT: L 172 ASP cc_start: 0.7460 (p0) cc_final: 0.6992 (p0) REVERT: L 175 ASP cc_start: 0.8337 (t0) cc_final: 0.8027 (t0) outliers start: 32 outliers final: 14 residues processed: 143 average time/residue: 0.5390 time to fit residues: 82.5201 Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 44 GLN B 96 ASN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN L 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069881 restraints weight = 19672.609| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.04 r_work: 0.2910 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8807 Z= 0.144 Angle : 0.597 10.888 11979 Z= 0.296 Chirality : 0.042 0.182 1349 Planarity : 0.004 0.041 1506 Dihedral : 3.847 27.026 1178 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.72 % Allowed : 20.48 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1072 helix: 2.17 (0.26), residues: 411 sheet: 0.48 (0.31), residues: 253 loop : -0.08 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.017 0.001 TYR C 107 PHE 0.012 0.001 PHE C 93 TRP 0.010 0.001 TRP C 233 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8805) covalent geometry : angle 0.59639 / 0.30 (11975) SS BOND : bond 0.00099 / 0.05 ( 2) SS BOND : angle 0.90258 / 0.50 ( 4) hydrogen bonds : bond 0.03247 / 2.24 ( 457) hydrogen bonds : angle 4.16566 / 3.05 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.348 Fit side-chains REVERT: A 160 GLN cc_start: 0.8728 (mm110) cc_final: 0.8235 (tt0) REVERT: A 222 GLN cc_start: 0.8888 (tt0) cc_final: 0.8376 (tp-100) REVERT: A 267 GLU cc_start: 0.7786 (tt0) cc_final: 0.7276 (mm-30) REVERT: B 72 ASP cc_start: 0.7994 (t0) cc_final: 0.7354 (t0) REVERT: B 106 ASP cc_start: 0.9171 (p0) cc_final: 0.8911 (p0) REVERT: C 112 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7726 (mm-30) REVERT: C 350 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.7599 (t160) REVERT: C 356 GLN cc_start: 0.7231 (pt0) cc_final: 0.6803 (pt0) REVERT: H 93 MET cc_start: 0.8618 (tpp) cc_final: 0.8372 (tpp) REVERT: H 153 LYS cc_start: 0.7879 (tttm) cc_final: 0.7579 (tttp) REVERT: H 211 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8744 (mmmt) REVERT: H 216 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8713 (mmmm) REVERT: H 218 ASP cc_start: 0.8427 (t0) cc_final: 0.7989 (m-30) REVERT: L 51 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8824 (ptmm) REVERT: L 87 GLU cc_start: 0.9158 (pm20) cc_final: 0.8774 (pm20) REVERT: L 113 ARG cc_start: 0.8457 (ptm160) cc_final: 0.7836 (ptm-80) REVERT: L 121 PHE cc_start: 0.8041 (m-10) cc_final: 0.7815 (m-10) REVERT: L 172 ASP cc_start: 0.7419 (p0) cc_final: 0.7028 (p0) REVERT: L 175 ASP cc_start: 0.8217 (t0) cc_final: 0.7880 (t0) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 0.5525 time to fit residues: 83.2544 Evaluate side-chains 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 72 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 327 ASN B 44 GLN B 96 ASN C 350 ASN C 356 GLN H 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070906 restraints weight = 19670.749| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.06 r_work: 0.2934 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8807 Z= 0.119 Angle : 0.617 11.338 11979 Z= 0.302 Chirality : 0.041 0.186 1349 Planarity : 0.004 0.029 1506 Dihedral : 3.760 19.312 1178 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.61 % Allowed : 20.70 % Favored : 76.69 % 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: 1.44 (0.26), residues: 1072 helix: 2.31 (0.26), residues: 405 sheet: 0.49 (0.31), residues: 253 loop : -0.04 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.012 0.001 TYR B 109 PHE 0.031 0.001 PHE L 144 TRP 0.011 0.001 TRP C 233 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8805) covalent geometry : angle 0.61734 / 0.30 (11975) SS BOND : bond 0.00212 / 0.11 ( 2) SS BOND : angle 0.97328 / 0.54 ( 4) hydrogen bonds : bond 0.02986 / 2.05 ( 457) hydrogen bonds : angle 4.08148 / 2.98 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8696 (mm110) cc_final: 0.8201 (tt0) REVERT: A 222 GLN cc_start: 0.8876 (tt0) cc_final: 0.8406 (tp40) REVERT: A 267 GLU cc_start: 0.7787 (tt0) cc_final: 0.7348 (mm-30) REVERT: A 339 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8463 (mtmm) REVERT: B 72 ASP cc_start: 0.7951 (t0) cc_final: 0.7302 (t0) REVERT: B 106 ASP cc_start: 0.9147 (p0) cc_final: 0.8907 (p0) REVERT: C 112 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7723 (mm-30) REVERT: C 350 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7702 (t0) REVERT: H 93 MET cc_start: 0.8586 (tpp) cc_final: 0.8326 (tpp) REVERT: H 150 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8327 (p) REVERT: H 153 LYS cc_start: 0.7909 (tttm) cc_final: 0.7585 (tttp) REVERT: H 211 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8750 (mmmt) REVERT: H 216 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: H 218 ASP cc_start: 0.8414 (t0) cc_final: 0.8010 (m-30) REVERT: L 51 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8812 (ptmm) REVERT: L 87 GLU cc_start: 0.9131 (pm20) cc_final: 0.8724 (pm20) REVERT: L 121 PHE cc_start: 0.8130 (m-10) cc_final: 0.7883 (m-10) REVERT: L 172 ASP cc_start: 0.7431 (p0) cc_final: 0.7046 (p0) REVERT: L 175 ASP cc_start: 0.8220 (t0) cc_final: 0.7803 (t0) outliers start: 24 outliers final: 11 residues processed: 140 average time/residue: 0.5477 time to fit residues: 82.0406 Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 96 ASN C 350 ASN H 13 GLN ** L 1 ASN ** 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 = 0.3618 r_free = 0.3618 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070480 restraints weight = 19944.524| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.06 r_work: 0.2929 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8807 Z= 0.120 Angle : 0.624 11.476 11979 Z= 0.306 Chirality : 0.041 0.185 1349 Planarity : 0.003 0.028 1506 Dihedral : 3.744 19.667 1178 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.96 % Allowed : 22.44 % Favored : 75.60 % 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: 1.39 (0.26), residues: 1072 helix: 2.23 (0.26), residues: 405 sheet: 0.52 (0.31), residues: 253 loop : -0.07 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.015 0.001 TYR C 107 PHE 0.030 0.001 PHE L 144 TRP 0.012 0.001 TRP C 233 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8805) covalent geometry : angle 0.62382 / 0.31 (11975) SS BOND : bond 0.00070 / 0.04 ( 2) SS BOND : angle 0.81544 / 0.45 ( 4) hydrogen bonds : bond 0.02979 / 2.03 ( 457) hydrogen bonds : angle 4.05413 / 2.96 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.357 Fit side-chains REVERT: A 160 GLN cc_start: 0.8680 (mm110) cc_final: 0.8218 (OUTLIER) REVERT: A 222 GLN cc_start: 0.8890 (tt0) cc_final: 0.8429 (tp40) REVERT: A 267 GLU cc_start: 0.7769 (tt0) cc_final: 0.7363 (mm-30) REVERT: A 339 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8492 (mtmt) REVERT: B 72 ASP cc_start: 0.7936 (t0) cc_final: 0.7308 (t0) REVERT: B 106 ASP cc_start: 0.9114 (p0) cc_final: 0.8891 (p0) REVERT: C 112 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7779 (mm-30) REVERT: C 350 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.7935 (t0) REVERT: C 355 ARG cc_start: 0.8611 (ptp90) cc_final: 0.8240 (ptt-90) REVERT: H 93 MET cc_start: 0.8653 (tpp) cc_final: 0.8416 (tpp) REVERT: H 150 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8365 (p) REVERT: H 153 LYS cc_start: 0.8046 (tttm) cc_final: 0.7713 (tttp) REVERT: H 211 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8765 (mmmt) REVERT: H 216 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8702 (mmmm) REVERT: H 218 ASP cc_start: 0.8427 (t0) cc_final: 0.7988 (m-30) REVERT: L 51 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8888 (ptmm) REVERT: L 87 GLU cc_start: 0.9159 (pm20) cc_final: 0.8794 (pm20) REVERT: L 121 PHE cc_start: 0.8197 (m-10) cc_final: 0.7977 (m-10) REVERT: L 172 ASP cc_start: 0.7530 (p0) cc_final: 0.7158 (p0) REVERT: L 175 ASP cc_start: 0.8201 (t0) cc_final: 0.7832 (t0) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.5771 time to fit residues: 80.6054 Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN B 96 ASN H 13 GLN ** L 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.070038 restraints weight = 19936.226| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.99 r_work: 0.2914 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8807 Z= 0.135 Angle : 0.627 11.540 11979 Z= 0.308 Chirality : 0.042 0.189 1349 Planarity : 0.003 0.028 1506 Dihedral : 3.785 20.597 1178 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.07 % Allowed : 22.66 % Favored : 75.27 % 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: 1.40 (0.26), residues: 1072 helix: 2.24 (0.26), residues: 405 sheet: 0.55 (0.32), residues: 253 loop : -0.09 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.017 0.001 TYR C 107 PHE 0.028 0.001 PHE L 144 TRP 0.013 0.001 TRP C 233 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8805) covalent geometry : angle 0.62672 / 0.31 (11975) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 0.85211 / 0.47 ( 4) hydrogen bonds : bond 0.03039 / 2.08 ( 457) hydrogen bonds : angle 4.09077 / 2.99 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.63 seconds wall clock time: 53 minutes 44.83 seconds (3224.83 seconds total)