Starting phenix.real_space_refine on Mon Jul 28 09:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdc_31913/07_2025/7vdc_31913.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 6.83, per 1000 atoms: 0.65 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.5, 81.25, 107.25, 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 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 54.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.956A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.829A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.635A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.937A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.657A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.816A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.728A pdb=" N ALA A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 37 through 46 removed outlier: 4.056A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 73 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.584A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.803A pdb=" N ARG B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 181 Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.582A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.784A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.498A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.077A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 66 through 73 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 159 through 181 Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.679A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.790A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.546A pdb=" N ALA C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.516A pdb=" N ARG C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.821A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.514A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 4.172A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.774A pdb=" N ARG D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 181 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.721A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.792A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.894A pdb=" N TYR A 301 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 152 removed outlier: 7.038A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.298A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 301 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.528A pdb=" N ILE C 185 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 144 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR C 301 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'D' and resid 296 through 297 removed outlier: 3.859A pdb=" N PHE D 144 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 301 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 112 through 114 537 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.93 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: 3503 1.34 - 1.46: 1330 1.46 - 1.57: 5782 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.44e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CG PRO A 158 " pdb=" CD PRO A 158 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.52e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.473 0.033 3.90e-02 6.57e+02 7.05e-01 bond pdb=" C THR A 343 " pdb=" O THR A 343 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.65e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 14113 1.43 - 2.86: 281 2.86 - 4.29: 57 4.29 - 5.72: 11 5.72 - 7.15: 2 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 108.01 3.99 1.40e+00 5.10e-01 8.11e+00 angle pdb=" N VAL A 260 " pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 107.76 110.60 -2.84 1.01e+00 9.80e-01 7.90e+00 angle pdb=" N GLY A 47 " pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 114.85 111.86 2.99 1.35e+00 5.49e-01 4.92e+00 angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 120.60 115.73 4.87 2.20e+00 2.07e-01 4.91e+00 angle pdb=" C LYS C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta sigma weight residual 121.58 117.50 4.08 1.95e+00 2.63e-01 4.38e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5759 16.81 - 33.61: 580 33.61 - 50.42: 125 50.42 - 67.23: 34 67.23 - 84.03: 6 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CG ARG D 172 " pdb=" CD ARG D 172 " pdb=" NE ARG D 172 " pdb=" CZ ARG D 172 " ideal model delta sinusoidal sigma weight residual 90.00 134.39 -44.39 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 257 " pdb=" CD ARG C 257 " pdb=" NE ARG C 257 " pdb=" CZ ARG C 257 " ideal model delta sinusoidal sigma weight residual -90.00 -133.53 43.53 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG C 172 " pdb=" CD ARG C 172 " pdb=" NE ARG C 172 " pdb=" CZ ARG C 172 " ideal model delta sinusoidal sigma weight residual 180.00 136.86 43.14 2 1.50e+01 4.44e-03 9.98e+00 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 980 0.027 - 0.054: 378 0.054 - 0.080: 169 0.080 - 0.107: 90 0.107 - 0.134: 27 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL B 23 " pdb=" CA VAL B 23 " pdb=" CG1 VAL B 23 " pdb=" CG2 VAL B 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE C 190 " pdb=" N ILE C 190 " pdb=" C ILE C 190 " pdb=" CB ILE C 190 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 157 " -0.063 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 158 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 187 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO D 188 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " -0.044 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 92 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.036 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 97 2.63 - 3.20: 9371 3.20 - 3.77: 16904 3.77 - 4.33: 22564 4.33 - 4.90: 37030 Nonbonded interactions: 85966 Sorted by model distance: nonbonded pdb=" O GLU C 224 " pdb=" OG1 THR C 265 " model vdw 2.066 3.040 nonbonded pdb=" O GLU D 224 " pdb=" OG1 THR D 265 " model vdw 2.075 3.040 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 265 " model vdw 2.155 3.040 nonbonded pdb=" O GLU B 224 " pdb=" OG1 THR B 265 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 275 " pdb=" OE1 GLU C 276 " model vdw 2.209 3.040 ... (remaining 85961 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' selection = chain 'D' } 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=0.00 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.002 0.087 10672 Z= 0.105 Angle : 0.516 7.148 14464 Z= 0.266 Chirality : 0.040 0.134 1644 Planarity : 0.005 0.097 1880 Dihedral : 14.497 84.033 3984 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.15 (0.23), residues: 1364 helix: 1.77 (0.19), residues: 672 sheet: -1.80 (0.31), residues: 248 loop : -1.30 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 295 HIS 0.002 0.000 HIS D 156 PHE 0.008 0.001 PHE C 144 TYR 0.014 0.002 TYR B 203 ARG 0.006 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.13271 ( 537) hydrogen bonds : angle 4.68638 ( 1569) covalent geometry : bond 0.00232 (10672) covalent geometry : angle 0.51632 (14464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.080 Fit side-chains REVERT: A 170 LEU cc_start: 0.8677 (mt) cc_final: 0.8449 (mt) REVERT: B 72 CYS cc_start: 0.6881 (m) cc_final: 0.6358 (t) REVERT: B 139 LYS cc_start: 0.7843 (pttt) cc_final: 0.6882 (ttpt) REVERT: C 130 LEU cc_start: 0.7920 (tp) cc_final: 0.7701 (tp) REVERT: C 139 LYS cc_start: 0.7884 (pttt) cc_final: 0.6888 (ttpt) REVERT: C 298 THR cc_start: 0.7512 (m) cc_final: 0.6974 (p) REVERT: D 189 GLU cc_start: 0.7332 (tp30) cc_final: 0.7121 (tp30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2250 time to fit residues: 87.9184 Evaluate side-chains 229 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.0040 chunk 123 optimal weight: 3.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.190897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150492 restraints weight = 12465.636| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.43 r_work: 0.3711 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.134 Angle : 0.543 6.355 14464 Z= 0.275 Chirality : 0.041 0.144 1644 Planarity : 0.005 0.059 1880 Dihedral : 3.670 15.185 1472 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.90 % Allowed : 8.54 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.23), residues: 1364 helix: 1.96 (0.19), residues: 676 sheet: -1.92 (0.41), residues: 152 loop : -1.39 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 PHE 0.015 0.002 PHE C 144 TYR 0.020 0.002 TYR A 58 ARG 0.003 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 537) hydrogen bonds : angle 3.75074 ( 1569) covalent geometry : bond 0.00310 (10672) covalent geometry : angle 0.54257 (14464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7555 (pttt) cc_final: 0.7235 (ttpt) REVERT: A 298 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7110 (p) REVERT: C 130 LEU cc_start: 0.7978 (tp) cc_final: 0.7722 (tp) REVERT: D 139 LYS cc_start: 0.7784 (pttp) cc_final: 0.7351 (pttt) outliers start: 10 outliers final: 9 residues processed: 248 average time/residue: 0.2531 time to fit residues: 85.6399 Evaluate side-chains 235 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151090 restraints weight = 12473.779| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.39 r_work: 0.3717 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.113 Angle : 0.505 6.739 14464 Z= 0.256 Chirality : 0.040 0.139 1644 Planarity : 0.005 0.049 1880 Dihedral : 3.619 14.884 1472 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.44 % Allowed : 10.34 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 676 sheet: -1.68 (0.41), residues: 144 loop : -1.48 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 PHE 0.012 0.001 PHE D 144 TYR 0.020 0.002 TYR A 58 ARG 0.002 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 537) hydrogen bonds : angle 3.56050 ( 1569) covalent geometry : bond 0.00258 (10672) covalent geometry : angle 0.50482 (14464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 1.161 Fit side-chains REVERT: A 114 PRO cc_start: 0.8026 (Cg_endo) cc_final: 0.7747 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7601 (pttt) cc_final: 0.7209 (ttpt) REVERT: A 298 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7052 (p) REVERT: B 170 LEU cc_start: 0.8744 (mt) cc_final: 0.8488 (mt) REVERT: C 130 LEU cc_start: 0.7989 (tp) cc_final: 0.7720 (tp) outliers start: 16 outliers final: 14 residues processed: 247 average time/residue: 0.2477 time to fit residues: 83.4956 Evaluate side-chains 235 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS D 2 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.192379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153757 restraints weight = 12315.154| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.33 r_work: 0.3749 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10672 Z= 0.095 Angle : 0.479 7.029 14464 Z= 0.242 Chirality : 0.039 0.136 1644 Planarity : 0.004 0.047 1880 Dihedral : 3.477 14.508 1472 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.53 % Allowed : 12.32 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.23), residues: 1364 helix: 2.23 (0.19), residues: 676 sheet: -1.62 (0.40), residues: 152 loop : -1.33 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 PHE 0.011 0.001 PHE C 144 TYR 0.019 0.002 TYR A 58 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 537) hydrogen bonds : angle 3.43597 ( 1569) covalent geometry : bond 0.00209 (10672) covalent geometry : angle 0.47949 (14464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 1.082 Fit side-chains REVERT: A 114 PRO cc_start: 0.8004 (Cg_endo) cc_final: 0.7736 (Cg_exo) REVERT: A 170 LEU cc_start: 0.8787 (mt) cc_final: 0.8569 (mt) REVERT: A 298 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 325 GLU cc_start: 0.8223 (tt0) cc_final: 0.7935 (mt-10) REVERT: B 72 CYS cc_start: 0.7323 (m) cc_final: 0.6675 (t) REVERT: B 170 LEU cc_start: 0.8709 (mt) cc_final: 0.8454 (mt) REVERT: B 189 GLU cc_start: 0.7320 (tp30) cc_final: 0.7029 (tp30) REVERT: C 130 LEU cc_start: 0.7967 (tp) cc_final: 0.7687 (tp) REVERT: C 170 LEU cc_start: 0.8740 (mt) cc_final: 0.8521 (mt) REVERT: C 298 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7058 (p) REVERT: D 139 LYS cc_start: 0.7734 (pttp) cc_final: 0.7479 (pttt) REVERT: D 170 LEU cc_start: 0.8782 (mt) cc_final: 0.8530 (mt) outliers start: 17 outliers final: 14 residues processed: 255 average time/residue: 0.2523 time to fit residues: 87.4926 Evaluate side-chains 249 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 94 optimal weight: 0.0060 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS D 11 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.192456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153078 restraints weight = 12453.757| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.44 r_work: 0.3737 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10672 Z= 0.120 Angle : 0.498 7.076 14464 Z= 0.253 Chirality : 0.040 0.142 1644 Planarity : 0.004 0.050 1880 Dihedral : 3.531 14.235 1472 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.53 % Allowed : 14.48 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.63 (0.23), residues: 1364 helix: 2.24 (0.19), residues: 676 sheet: -1.69 (0.40), residues: 152 loop : -1.37 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 PHE 0.014 0.001 PHE C 144 TYR 0.018 0.002 TYR A 58 ARG 0.005 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 537) hydrogen bonds : angle 3.41132 ( 1569) covalent geometry : bond 0.00278 (10672) covalent geometry : angle 0.49791 (14464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 1.177 Fit side-chains REVERT: A 114 PRO cc_start: 0.7988 (Cg_endo) cc_final: 0.7716 (Cg_exo) REVERT: A 298 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.6989 (p) REVERT: B 170 LEU cc_start: 0.8790 (mt) cc_final: 0.8526 (mt) REVERT: B 189 GLU cc_start: 0.7419 (tp30) cc_final: 0.7009 (tp30) REVERT: C 130 LEU cc_start: 0.7997 (tp) cc_final: 0.7736 (tp) REVERT: C 298 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7075 (p) REVERT: D 139 LYS cc_start: 0.7833 (pttp) cc_final: 0.7613 (pttp) REVERT: D 320 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6075 (mp) outliers start: 17 outliers final: 13 residues processed: 241 average time/residue: 0.2435 time to fit residues: 80.7430 Evaluate side-chains 237 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** 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 = 0.4279 r_free = 0.4279 target = 0.190381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150719 restraints weight = 12572.597| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.45 r_work: 0.3712 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.148 Angle : 0.532 6.932 14464 Z= 0.273 Chirality : 0.041 0.145 1644 Planarity : 0.005 0.054 1880 Dihedral : 3.699 14.268 1472 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.34 % Allowed : 14.66 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.48 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 676 sheet: -1.78 (0.39), residues: 152 loop : -1.44 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 147 HIS 0.010 0.001 HIS C 2 PHE 0.015 0.002 PHE C 144 TYR 0.023 0.002 TYR A 58 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 537) hydrogen bonds : angle 3.47305 ( 1569) covalent geometry : bond 0.00348 (10672) covalent geometry : angle 0.53210 (14464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.102 Fit side-chains REVERT: A 114 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7721 (Cg_exo) REVERT: A 330 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7866 (mmm160) REVERT: B 189 GLU cc_start: 0.7521 (tp30) cc_final: 0.7103 (tp30) REVERT: C 130 LEU cc_start: 0.8038 (tp) cc_final: 0.7817 (tp) REVERT: C 342 TYR cc_start: 0.6832 (t80) cc_final: 0.6425 (t80) REVERT: D 320 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6039 (mp) outliers start: 26 outliers final: 21 residues processed: 244 average time/residue: 0.2564 time to fit residues: 86.3871 Evaluate side-chains 240 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** 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 = 0.4299 r_free = 0.4299 target = 0.192343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.153168 restraints weight = 12658.237| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.46 r_work: 0.3743 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10672 Z= 0.107 Angle : 0.498 7.633 14464 Z= 0.253 Chirality : 0.040 0.139 1644 Planarity : 0.004 0.054 1880 Dihedral : 3.571 14.138 1472 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.53 % Allowed : 16.91 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1364 helix: 2.21 (0.19), residues: 676 sheet: -1.94 (0.38), residues: 160 loop : -1.27 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.010 0.001 HIS C 2 PHE 0.011 0.001 PHE C 144 TYR 0.022 0.002 TYR A 58 ARG 0.002 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 537) hydrogen bonds : angle 3.38355 ( 1569) covalent geometry : bond 0.00244 (10672) covalent geometry : angle 0.49755 (14464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 1.263 Fit side-chains REVERT: A 114 PRO cc_start: 0.7961 (Cg_endo) cc_final: 0.7675 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7877 (pttt) cc_final: 0.6809 (ttpt) REVERT: A 330 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7807 (mmm160) REVERT: B 72 CYS cc_start: 0.7379 (m) cc_final: 0.6685 (t) REVERT: B 110 LYS cc_start: 0.6888 (mmmt) cc_final: 0.6531 (mmtt) REVERT: B 139 LYS cc_start: 0.7926 (pttt) cc_final: 0.6896 (ttpt) REVERT: B 170 LEU cc_start: 0.8764 (mt) cc_final: 0.8498 (mt) REVERT: B 189 GLU cc_start: 0.7455 (tp30) cc_final: 0.7048 (tp30) REVERT: C 130 LEU cc_start: 0.8010 (tp) cc_final: 0.7764 (tp) REVERT: C 330 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.6531 (mmm-85) REVERT: C 342 TYR cc_start: 0.6873 (t80) cc_final: 0.6559 (t80) REVERT: D 170 LEU cc_start: 0.8794 (mt) cc_final: 0.8554 (mt) REVERT: D 320 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6047 (mp) outliers start: 17 outliers final: 13 residues processed: 246 average time/residue: 0.2538 time to fit residues: 86.3569 Evaluate side-chains 235 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 0.0050 chunk 109 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151947 restraints weight = 12561.941| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.43 r_work: 0.3729 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.130 Angle : 0.523 7.833 14464 Z= 0.267 Chirality : 0.041 0.144 1644 Planarity : 0.005 0.057 1880 Dihedral : 3.617 14.408 1472 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.89 % Allowed : 17.00 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.53 (0.23), residues: 1364 helix: 2.14 (0.19), residues: 676 sheet: -1.98 (0.38), residues: 160 loop : -1.28 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 147 HIS 0.010 0.001 HIS C 2 PHE 0.014 0.002 PHE C 144 TYR 0.022 0.002 TYR A 58 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 537) hydrogen bonds : angle 3.42153 ( 1569) covalent geometry : bond 0.00304 (10672) covalent geometry : angle 0.52308 (14464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.181 Fit side-chains REVERT: A 114 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7686 (Cg_exo) REVERT: B 110 LYS cc_start: 0.6901 (mmmt) cc_final: 0.6573 (mmtt) REVERT: B 170 LEU cc_start: 0.8793 (mt) cc_final: 0.8526 (mt) REVERT: B 189 GLU cc_start: 0.7476 (tp30) cc_final: 0.7067 (tp30) REVERT: C 130 LEU cc_start: 0.8040 (tp) cc_final: 0.7813 (tp) REVERT: C 139 LYS cc_start: 0.7899 (pttt) cc_final: 0.6825 (ttpt) REVERT: D 320 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6031 (mp) outliers start: 21 outliers final: 17 residues processed: 241 average time/residue: 0.3107 time to fit residues: 102.4422 Evaluate side-chains 243 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.192521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153337 restraints weight = 12693.193| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.47 r_work: 0.3742 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.108 Angle : 0.505 8.219 14464 Z= 0.257 Chirality : 0.040 0.139 1644 Planarity : 0.004 0.058 1880 Dihedral : 3.535 13.846 1472 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.80 % Allowed : 17.36 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.65 (0.23), residues: 1364 helix: 2.25 (0.19), residues: 676 sheet: -1.80 (0.34), residues: 200 loop : -1.20 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.010 0.001 HIS C 2 PHE 0.011 0.001 PHE C 144 TYR 0.022 0.002 TYR A 58 ARG 0.003 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 537) hydrogen bonds : angle 3.34226 ( 1569) covalent geometry : bond 0.00250 (10672) covalent geometry : angle 0.50492 (14464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.055 Fit side-chains REVERT: A 114 PRO cc_start: 0.7970 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7933 (pttt) cc_final: 0.6807 (ttpt) REVERT: A 330 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7227 (mmt180) REVERT: B 110 LYS cc_start: 0.6878 (mmmt) cc_final: 0.6566 (mmtt) REVERT: B 139 LYS cc_start: 0.7972 (pttt) cc_final: 0.6868 (ttpt) REVERT: B 170 LEU cc_start: 0.8762 (mt) cc_final: 0.8501 (mt) REVERT: B 189 GLU cc_start: 0.7473 (tp30) cc_final: 0.7065 (tp30) REVERT: C 130 LEU cc_start: 0.8021 (tp) cc_final: 0.7801 (tp) REVERT: C 170 LEU cc_start: 0.8773 (mt) cc_final: 0.8550 (mt) REVERT: C 330 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.6563 (mmm-85) REVERT: D 139 LYS cc_start: 0.7669 (pttp) cc_final: 0.6754 (ttpt) REVERT: D 170 LEU cc_start: 0.8786 (mt) cc_final: 0.8558 (mt) REVERT: D 320 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6039 (mp) outliers start: 20 outliers final: 16 residues processed: 246 average time/residue: 0.2723 time to fit residues: 93.3203 Evaluate side-chains 241 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152538 restraints weight = 12625.219| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.45 r_work: 0.3734 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.129 Angle : 0.524 8.186 14464 Z= 0.268 Chirality : 0.041 0.143 1644 Planarity : 0.005 0.060 1880 Dihedral : 3.591 14.371 1472 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.71 % Allowed : 17.63 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.56 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 676 sheet: -2.02 (0.33), residues: 208 loop : -1.12 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 147 HIS 0.010 0.001 HIS D 156 PHE 0.013 0.002 PHE C 144 TYR 0.026 0.002 TYR B 173 ARG 0.002 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 537) hydrogen bonds : angle 3.37040 ( 1569) covalent geometry : bond 0.00302 (10672) covalent geometry : angle 0.52444 (14464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.295 Fit side-chains REVERT: A 114 PRO cc_start: 0.7979 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7948 (pttt) cc_final: 0.6835 (ttpt) REVERT: A 330 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7240 (mmt180) REVERT: B 110 LYS cc_start: 0.6925 (mmmt) cc_final: 0.6623 (mmtt) REVERT: B 139 LYS cc_start: 0.8015 (pttt) cc_final: 0.6891 (ttpt) REVERT: B 170 LEU cc_start: 0.8764 (mt) cc_final: 0.8500 (mt) REVERT: B 189 GLU cc_start: 0.7481 (tp30) cc_final: 0.7077 (tp30) REVERT: C 130 LEU cc_start: 0.8032 (tp) cc_final: 0.7807 (tp) REVERT: C 139 LYS cc_start: 0.7925 (pttt) cc_final: 0.6863 (ttpt) REVERT: C 330 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.6566 (mmm-85) REVERT: D 320 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6034 (mp) outliers start: 19 outliers final: 18 residues processed: 229 average time/residue: 0.2672 time to fit residues: 82.8869 Evaluate side-chains 239 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 0.0040 chunk 38 optimal weight: 4.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** 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 = 0.4272 r_free = 0.4272 target = 0.189659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150434 restraints weight = 12532.909| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.44 r_work: 0.3712 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10672 Z= 0.165 Angle : 0.561 8.085 14464 Z= 0.288 Chirality : 0.042 0.149 1644 Planarity : 0.005 0.060 1880 Dihedral : 3.768 14.631 1472 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.16 % Allowed : 17.45 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.41 (0.23), residues: 1364 helix: 2.02 (0.19), residues: 676 sheet: -2.03 (0.37), residues: 160 loop : -1.32 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 147 HIS 0.011 0.001 HIS D 156 PHE 0.016 0.002 PHE D 144 TYR 0.022 0.003 TYR A 213 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 537) hydrogen bonds : angle 3.45714 ( 1569) covalent geometry : bond 0.00387 (10672) covalent geometry : angle 0.56108 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5043.37 seconds wall clock time: 88 minutes 53.64 seconds (5333.64 seconds total)