Starting phenix.real_space_refine on Fri Jun 6 05:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4f_25675/06_2025/7t4f_25675.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4516 2.51 5 N 1216 2.21 5 O 1472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7224 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "C" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "D" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Time building chain proxies: 5.35, per 1000 atoms: 0.74 Number of scatterers: 7224 At special positions: 0 Unit cell: (108.9, 108.9, 127.6, 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 20 16.00 O 1472 8.00 N 1216 7.00 C 4516 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: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 8.2% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.556A pdb=" N SER B 156 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.504A pdb=" N SER C 156 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.601A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 131 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL A 136 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.601A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 17.808A pdb=" N ARG A 121 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 14.231A pdb=" N ASP C 56 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N TRP A 123 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER C 54 " --> pdb=" O TRP A 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 125 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 51 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C 75 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU C 53 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.744A pdb=" N THR A 51 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 75 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.687A pdb=" N THR A 171 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 244 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 173 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.449A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 129 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 138 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 44 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 85 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 42 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.449A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 17.775A pdb=" N ARG B 121 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 14.331A pdb=" N ASP D 56 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N TRP B 123 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N SER D 54 " --> pdb=" O TRP B 123 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B 125 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 51 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS D 75 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU D 53 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.715A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR B 171 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 244 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 173 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 36 through 38 removed outlier: 5.478A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS C 142 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 127 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 140 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 129 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C 138 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 131 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL C 136 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER C 81 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 45 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 83 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR C 171 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR C 244 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 173 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 38 removed outlier: 5.322A pdb=" N ALA D 107 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 142 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 127 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR D 140 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS D 129 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR D 138 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 44 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA D 85 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL D 42 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 167 Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR D 171 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 244 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 173 " --> pdb=" O THR D 244 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1249 1.31 - 1.44: 1883 1.44 - 1.56: 4196 1.56 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7368 Sorted by residual: bond pdb=" C PRO B 9 " pdb=" O PRO B 9 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.16e-02 7.43e+03 1.55e+01 bond pdb=" C PRO D 9 " pdb=" O PRO D 9 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.37e+01 bond pdb=" N VAL D 10 " pdb=" CA VAL D 10 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL C 10 " pdb=" CA VAL C 10 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA ALA A 13 " pdb=" CB ALA A 13 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.44e-02 4.82e+03 1.20e+01 ... (remaining 7363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9700 1.78 - 3.55: 305 3.55 - 5.33: 49 5.33 - 7.11: 8 7.11 - 8.88: 2 Bond angle restraints: 10064 Sorted by residual: angle pdb=" N GLY B 12 " pdb=" CA GLY B 12 " pdb=" C GLY B 12 " ideal model delta sigma weight residual 114.67 121.24 -6.57 1.10e+00 8.26e-01 3.57e+01 angle pdb=" N PRO D 9 " pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " ideal model delta sigma weight residual 103.35 98.89 4.46 8.70e-01 1.32e+00 2.62e+01 angle pdb=" C THR C 15 " pdb=" CA THR C 15 " pdb=" CB THR C 15 " ideal model delta sigma weight residual 109.53 117.59 -8.06 1.69e+00 3.50e-01 2.27e+01 angle pdb=" C LYS C 11 " pdb=" CA LYS C 11 " pdb=" CB LYS C 11 " ideal model delta sigma weight residual 109.68 118.56 -8.88 2.05e+00 2.38e-01 1.88e+01 angle pdb=" C GLY B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta sigma weight residual 121.83 128.46 -6.63 1.56e+00 4.11e-01 1.81e+01 ... (remaining 10059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3958 17.68 - 35.35: 298 35.35 - 53.02: 71 53.02 - 70.70: 24 70.70 - 88.37: 9 Dihedral angle restraints: 4360 sinusoidal: 1588 harmonic: 2772 Sorted by residual: dihedral pdb=" CA ASP C 64 " pdb=" CB ASP C 64 " pdb=" CG ASP C 64 " pdb=" OD1 ASP C 64 " ideal model delta sinusoidal sigma weight residual -30.00 -87.53 57.53 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU C 135 " pdb=" CG GLU C 135 " pdb=" CD GLU C 135 " pdb=" OE1 GLU C 135 " ideal model delta sinusoidal sigma weight residual 0.00 -88.37 88.37 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG B 139 " pdb=" CD ARG B 139 " pdb=" NE ARG B 139 " pdb=" CZ ARG B 139 " ideal model delta sinusoidal sigma weight residual -90.00 -133.84 43.84 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 883 0.046 - 0.092: 177 0.092 - 0.138: 110 0.138 - 0.184: 14 0.184 - 0.230: 8 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA VAL C 228 " pdb=" N VAL C 228 " pdb=" C VAL C 228 " pdb=" CB VAL C 228 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL B 10 " pdb=" N VAL B 10 " pdb=" C VAL B 10 " pdb=" CB VAL B 10 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1189 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 13 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ALA B 13 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA B 13 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 14 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 14 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLY B 14 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 14 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 15 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 13 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ALA D 13 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA D 13 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY D 14 " -0.012 2.00e-02 2.50e+03 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 901 2.76 - 3.30: 6247 3.30 - 3.83: 11438 3.83 - 4.37: 12925 4.37 - 4.90: 23496 Nonbonded interactions: 55007 Sorted by model distance: nonbonded pdb=" OH TYR B 108 " pdb=" OD1 ASN B 145 " model vdw 2.228 3.040 nonbonded pdb=" ND2 ASN A 29 " pdb=" OD1 ASP A 192 " model vdw 2.247 3.120 nonbonded pdb=" OG SER A 126 " pdb=" OE2 GLU C 49 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OD1 ASN A 145 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 32 " pdb=" OG SER B 194 " model vdw 2.337 3.040 ... (remaining 55002 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: 0.02 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 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 : 0.004 0.050 7368 Z= 0.320 Angle : 0.701 8.884 10064 Z= 0.474 Chirality : 0.052 0.230 1192 Planarity : 0.004 0.043 1292 Dihedral : 14.605 88.374 2584 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.44 % Allowed : 12.18 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.54 (0.25), residues: 972 helix: 2.35 (0.64), residues: 54 sheet: 1.09 (0.23), residues: 494 loop : -0.82 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 123 PHE 0.010 0.001 PHE B 82 TYR 0.007 0.001 TYR A 108 ARG 0.004 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.16742 ( 269) hydrogen bonds : angle 6.85127 ( 768) covalent geometry : bond 0.00441 ( 7368) covalent geometry : angle 0.70126 (10064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.001 Fit side-chains REVERT: A 8 MET cc_start: 0.8167 (mtm) cc_final: 0.7897 (mtm) REVERT: A 11 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.7037 (mmmt) REVERT: B 11 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.6947 (mmpt) REVERT: C 31 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8864 (mm) REVERT: C 148 ARG cc_start: 0.8413 (ttt180) cc_final: 0.6756 (mmp80) REVERT: D 43 LYS cc_start: 0.8722 (mtpp) cc_final: 0.7805 (mmtm) REVERT: D 151 MET cc_start: 0.9054 (mmm) cc_final: 0.8804 (mmm) outliers start: 19 outliers final: 7 residues processed: 108 average time/residue: 1.2550 time to fit residues: 143.3916 Evaluate side-chains 98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.195094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108377 restraints weight = 7753.388| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.35 r_work: 0.3131 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7368 Z= 0.150 Angle : 0.517 4.795 10064 Z= 0.277 Chirality : 0.047 0.154 1192 Planarity : 0.004 0.031 1292 Dihedral : 5.444 56.705 1048 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.31 % Allowed : 12.44 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.25), residues: 972 helix: 1.93 (0.70), residues: 56 sheet: 1.04 (0.23), residues: 494 loop : -0.83 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 18 PHE 0.017 0.002 PHE A 120 TYR 0.010 0.001 TYR B 108 ARG 0.002 0.000 ARG C 155 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 269) hydrogen bonds : angle 5.33184 ( 768) covalent geometry : bond 0.00363 ( 7368) covalent geometry : angle 0.51684 (10064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.719 Fit side-chains REVERT: A 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8142 (ttt90) REVERT: B 11 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.7326 (mmpt) REVERT: B 63 GLU cc_start: 0.7091 (pm20) cc_final: 0.6845 (pt0) REVERT: B 91 GLN cc_start: 0.8738 (mm110) cc_final: 0.8429 (mm110) REVERT: C 43 LYS cc_start: 0.8837 (mtpp) cc_final: 0.7416 (mmtt) REVERT: C 134 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8337 (mtpm) REVERT: C 148 ARG cc_start: 0.8622 (ttt180) cc_final: 0.6379 (tpp-160) REVERT: D 5 ASN cc_start: 0.7567 (t0) cc_final: 0.7298 (t0) REVERT: D 43 LYS cc_start: 0.8776 (mtpp) cc_final: 0.7670 (mmtm) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 1.4533 time to fit residues: 135.5304 Evaluate side-chains 94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.191484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104997 restraints weight = 7839.269| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.39 r_work: 0.3071 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 7368 Z= 0.336 Angle : 0.674 8.157 10064 Z= 0.360 Chirality : 0.053 0.173 1192 Planarity : 0.006 0.042 1292 Dihedral : 5.322 57.461 1034 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.33 % Allowed : 12.31 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.05 (0.25), residues: 972 helix: 1.23 (0.72), residues: 56 sheet: 0.68 (0.22), residues: 506 loop : -0.95 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 67 PHE 0.029 0.003 PHE A 120 TYR 0.012 0.002 TYR B 108 ARG 0.004 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 269) hydrogen bonds : angle 5.51560 ( 768) covalent geometry : bond 0.00846 ( 7368) covalent geometry : angle 0.67382 (10064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.786 Fit side-chains REVERT: A 38 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8055 (ttt90) REVERT: B 11 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.7356 (mmpt) REVERT: B 41 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8772 (mttp) REVERT: B 91 GLN cc_start: 0.8736 (mm110) cc_final: 0.8351 (mm110) REVERT: C 31 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 43 LYS cc_start: 0.8872 (mtpp) cc_final: 0.7578 (mmtt) REVERT: C 134 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8308 (mtpm) REVERT: C 148 ARG cc_start: 0.8507 (ttt180) cc_final: 0.6248 (tpp-160) REVERT: C 151 MET cc_start: 0.8846 (mmp) cc_final: 0.8629 (mmp) REVERT: D 5 ASN cc_start: 0.7626 (t0) cc_final: 0.7321 (t0) REVERT: D 43 LYS cc_start: 0.8742 (mtpp) cc_final: 0.7596 (mmtm) REVERT: D 135 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (mt-10) outliers start: 26 outliers final: 12 residues processed: 88 average time/residue: 1.5703 time to fit residues: 144.4975 Evaluate side-chains 88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 135 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.0020 chunk 44 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 59 optimal weight: 0.0770 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.196582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110755 restraints weight = 7841.848| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.38 r_work: 0.3170 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7368 Z= 0.077 Angle : 0.427 6.170 10064 Z= 0.228 Chirality : 0.044 0.145 1192 Planarity : 0.004 0.039 1292 Dihedral : 4.387 59.431 1034 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.79 % Allowed : 14.23 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.21 (0.25), residues: 972 helix: 1.92 (0.70), residues: 56 sheet: 0.67 (0.22), residues: 516 loop : -0.79 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 18 PHE 0.012 0.001 PHE D 82 TYR 0.006 0.001 TYR B 108 ARG 0.002 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.02676 ( 269) hydrogen bonds : angle 4.63886 ( 768) covalent geometry : bond 0.00172 ( 7368) covalent geometry : angle 0.42677 (10064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.249 Fit side-chains REVERT: B 11 LYS cc_start: 0.8882 (mmmm) cc_final: 0.7478 (mmpt) REVERT: B 44 ASP cc_start: 0.8232 (m-30) cc_final: 0.7998 (m-30) REVERT: B 91 GLN cc_start: 0.8677 (mm110) cc_final: 0.8337 (mm110) REVERT: C 31 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8679 (mm) REVERT: C 43 LYS cc_start: 0.8770 (mtpp) cc_final: 0.7352 (mmtt) REVERT: C 148 ARG cc_start: 0.8551 (ttt180) cc_final: 0.6386 (tpp-160) REVERT: D 5 ASN cc_start: 0.7697 (t0) cc_final: 0.7355 (t0) REVERT: D 29 ASN cc_start: 0.8681 (t0) cc_final: 0.8436 (t0) REVERT: D 43 LYS cc_start: 0.8693 (mtpp) cc_final: 0.7601 (mmtm) outliers start: 14 outliers final: 4 residues processed: 94 average time/residue: 1.7054 time to fit residues: 168.3820 Evaluate side-chains 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.195674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109702 restraints weight = 7782.678| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.37 r_work: 0.3150 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7368 Z= 0.102 Angle : 0.451 6.449 10064 Z= 0.239 Chirality : 0.045 0.148 1192 Planarity : 0.004 0.040 1292 Dihedral : 4.107 59.814 1030 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.79 % Allowed : 15.38 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.37 (0.26), residues: 972 helix: 1.99 (0.69), residues: 56 sheet: 0.79 (0.23), residues: 510 loop : -0.68 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 18 PHE 0.012 0.001 PHE A 120 TYR 0.008 0.001 TYR B 108 ARG 0.001 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 269) hydrogen bonds : angle 4.61921 ( 768) covalent geometry : bond 0.00244 ( 7368) covalent geometry : angle 0.45069 (10064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.767 Fit side-chains REVERT: B 11 LYS cc_start: 0.8881 (mmmm) cc_final: 0.7435 (mmpt) REVERT: B 63 GLU cc_start: 0.7238 (pm20) cc_final: 0.6925 (pt0) REVERT: B 91 GLN cc_start: 0.8654 (mm110) cc_final: 0.8255 (mm110) REVERT: C 31 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8677 (mm) REVERT: C 43 LYS cc_start: 0.8782 (mtpp) cc_final: 0.7422 (mmtt) REVERT: C 134 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8344 (mtpm) REVERT: C 148 ARG cc_start: 0.8562 (ttt180) cc_final: 0.6362 (tpp-160) REVERT: D 5 ASN cc_start: 0.7704 (t0) cc_final: 0.7337 (t0) REVERT: D 29 ASN cc_start: 0.8705 (t0) cc_final: 0.8416 (t0) REVERT: D 43 LYS cc_start: 0.8686 (mtpp) cc_final: 0.7597 (mmtm) outliers start: 14 outliers final: 7 residues processed: 86 average time/residue: 2.6019 time to fit residues: 235.2340 Evaluate side-chains 85 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 94 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106645 restraints weight = 7797.545| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.36 r_work: 0.3119 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7368 Z= 0.164 Angle : 0.512 7.068 10064 Z= 0.270 Chirality : 0.047 0.158 1192 Planarity : 0.004 0.041 1292 Dihedral : 4.400 59.869 1030 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.05 % Allowed : 15.51 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.25 (0.26), residues: 972 helix: 1.73 (0.69), residues: 56 sheet: 0.75 (0.23), residues: 512 loop : -0.80 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 18 PHE 0.018 0.002 PHE A 120 TYR 0.010 0.001 TYR B 108 ARG 0.002 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 269) hydrogen bonds : angle 4.82596 ( 768) covalent geometry : bond 0.00407 ( 7368) covalent geometry : angle 0.51185 (10064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 2.771 Fit side-chains REVERT: A 38 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8017 (ttt90) REVERT: B 11 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.7412 (mmpt) REVERT: B 91 GLN cc_start: 0.8665 (mm110) cc_final: 0.8271 (mm110) REVERT: C 31 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 43 LYS cc_start: 0.8844 (mtpp) cc_final: 0.7573 (mmtt) REVERT: C 134 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8292 (mtpm) REVERT: C 148 ARG cc_start: 0.8530 (ttt180) cc_final: 0.6323 (tpp-160) REVERT: D 5 ASN cc_start: 0.7694 (t0) cc_final: 0.7323 (t0) REVERT: D 29 ASN cc_start: 0.8768 (t0) cc_final: 0.8508 (t0) REVERT: D 43 LYS cc_start: 0.8693 (mtpp) cc_final: 0.7592 (mmtm) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 2.7011 time to fit residues: 241.8759 Evaluate side-chains 87 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 71 optimal weight: 40.0000 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 56 optimal weight: 0.7980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.192654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106669 restraints weight = 7774.728| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.36 r_work: 0.3123 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7368 Z= 0.164 Angle : 0.509 6.745 10064 Z= 0.270 Chirality : 0.047 0.157 1192 Planarity : 0.005 0.041 1292 Dihedral : 4.415 58.911 1030 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.44 % Allowed : 16.03 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.27 (0.26), residues: 972 helix: 1.70 (0.69), residues: 56 sheet: 0.78 (0.23), residues: 496 loop : -0.75 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 18 PHE 0.018 0.002 PHE A 120 TYR 0.009 0.001 TYR B 108 ARG 0.002 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 269) hydrogen bonds : angle 4.82597 ( 768) covalent geometry : bond 0.00407 ( 7368) covalent geometry : angle 0.50915 (10064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.907 Fit side-chains REVERT: A 38 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8063 (ttt90) REVERT: B 11 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.7459 (mmpt) REVERT: B 91 GLN cc_start: 0.8744 (mm110) cc_final: 0.8368 (mm110) REVERT: C 31 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8715 (mm) REVERT: C 43 LYS cc_start: 0.8813 (mtpp) cc_final: 0.7540 (mmtt) REVERT: C 134 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8311 (mtpm) REVERT: C 148 ARG cc_start: 0.8558 (ttt180) cc_final: 0.6376 (tpp-160) REVERT: D 5 ASN cc_start: 0.7748 (t0) cc_final: 0.7395 (t0) REVERT: D 29 ASN cc_start: 0.8838 (t0) cc_final: 0.8563 (t0) REVERT: D 43 LYS cc_start: 0.8718 (mtpp) cc_final: 0.7637 (mmtm) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 1.6555 time to fit residues: 155.9931 Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.192564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.106638 restraints weight = 7925.737| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.38 r_work: 0.3106 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7368 Z= 0.223 Angle : 0.570 6.959 10064 Z= 0.301 Chirality : 0.049 0.164 1192 Planarity : 0.005 0.042 1292 Dihedral : 4.676 59.757 1030 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.44 % Allowed : 16.03 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.13 (0.26), residues: 972 helix: 1.45 (0.69), residues: 56 sheet: 0.72 (0.23), residues: 496 loop : -0.87 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 18 PHE 0.022 0.002 PHE A 120 TYR 0.010 0.001 TYR B 108 ARG 0.003 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 269) hydrogen bonds : angle 5.02166 ( 768) covalent geometry : bond 0.00557 ( 7368) covalent geometry : angle 0.56972 (10064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.723 Fit side-chains REVERT: A 31 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 38 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8027 (ttt90) REVERT: B 11 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.7459 (mmpt) REVERT: B 91 GLN cc_start: 0.8760 (mm110) cc_final: 0.8378 (mm110) REVERT: C 31 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8681 (mm) REVERT: C 41 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: C 43 LYS cc_start: 0.8838 (mtpp) cc_final: 0.7583 (mmtt) REVERT: C 134 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8315 (mtpm) REVERT: C 148 ARG cc_start: 0.8556 (ttt180) cc_final: 0.6327 (tpp-160) REVERT: D 5 ASN cc_start: 0.7771 (t0) cc_final: 0.7402 (t0) REVERT: D 43 LYS cc_start: 0.8710 (mtpp) cc_final: 0.7626 (mmtm) REVERT: D 53 GLU cc_start: 0.8494 (pt0) cc_final: 0.8283 (pt0) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 1.5088 time to fit residues: 137.3446 Evaluate side-chains 91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.191735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106002 restraints weight = 7835.232| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.33 r_work: 0.3107 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7368 Z= 0.200 Angle : 0.543 6.920 10064 Z= 0.288 Chirality : 0.048 0.158 1192 Planarity : 0.005 0.044 1292 Dihedral : 4.595 59.583 1030 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.11 (0.26), residues: 972 helix: 1.45 (0.70), residues: 56 sheet: 0.72 (0.24), residues: 496 loop : -0.91 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 18 PHE 0.020 0.002 PHE A 120 TYR 0.010 0.001 TYR B 108 ARG 0.002 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 269) hydrogen bonds : angle 4.96648 ( 768) covalent geometry : bond 0.00498 ( 7368) covalent geometry : angle 0.54326 (10064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.795 Fit side-chains REVERT: A 38 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8037 (ttt90) REVERT: B 11 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.7418 (mmpt) REVERT: B 91 GLN cc_start: 0.8733 (mm110) cc_final: 0.8349 (mm110) REVERT: C 31 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8661 (mm) REVERT: C 43 LYS cc_start: 0.8796 (mtpp) cc_final: 0.7507 (mmtt) REVERT: C 134 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8295 (mtpm) REVERT: C 148 ARG cc_start: 0.8537 (ttt180) cc_final: 0.6342 (tpp-160) REVERT: D 5 ASN cc_start: 0.7745 (t0) cc_final: 0.7386 (t0) REVERT: D 43 LYS cc_start: 0.8704 (mtpp) cc_final: 0.7605 (mmtm) outliers start: 20 outliers final: 14 residues processed: 87 average time/residue: 1.6345 time to fit residues: 148.9975 Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 chunk 41 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.191179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105236 restraints weight = 7963.783| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.40 r_work: 0.3099 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7368 Z= 0.235 Angle : 0.580 6.954 10064 Z= 0.307 Chirality : 0.049 0.162 1192 Planarity : 0.005 0.044 1292 Dihedral : 4.737 59.934 1030 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.18 % Allowed : 16.41 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.03 (0.26), residues: 972 helix: 1.35 (0.70), residues: 56 sheet: 0.69 (0.24), residues: 496 loop : -0.98 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 18 PHE 0.022 0.002 PHE A 120 TYR 0.010 0.001 TYR B 108 ARG 0.003 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 269) hydrogen bonds : angle 5.05878 ( 768) covalent geometry : bond 0.00590 ( 7368) covalent geometry : angle 0.58023 (10064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.428 Fit side-chains REVERT: A 38 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8016 (ttt90) REVERT: B 11 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7446 (mmpt) REVERT: B 91 GLN cc_start: 0.8759 (mm110) cc_final: 0.8376 (mm110) REVERT: C 31 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 43 LYS cc_start: 0.8826 (mtpp) cc_final: 0.7543 (mmtt) REVERT: C 134 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8311 (mtpm) REVERT: C 148 ARG cc_start: 0.8534 (ttt180) cc_final: 0.6341 (tpp-160) REVERT: D 5 ASN cc_start: 0.7786 (t0) cc_final: 0.7440 (t0) REVERT: D 43 LYS cc_start: 0.8717 (mtpp) cc_final: 0.7620 (mmtm) REVERT: D 53 GLU cc_start: 0.8500 (pt0) cc_final: 0.8290 (pt0) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 1.8841 time to fit residues: 171.4266 Evaluate side-chains 90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110662 restraints weight = 7803.044| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.35 r_work: 0.3155 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7368 Z= 0.078 Angle : 0.425 5.752 10064 Z= 0.226 Chirality : 0.045 0.147 1192 Planarity : 0.004 0.044 1292 Dihedral : 4.043 58.120 1030 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.15 % Allowed : 17.56 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.33 (0.26), residues: 972 helix: 1.92 (0.68), residues: 56 sheet: 0.84 (0.24), residues: 494 loop : -0.76 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 18 PHE 0.011 0.001 PHE B 82 TYR 0.005 0.001 TYR B 108 ARG 0.002 0.000 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 269) hydrogen bonds : angle 4.50761 ( 768) covalent geometry : bond 0.00181 ( 7368) covalent geometry : angle 0.42487 (10064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8767.33 seconds wall clock time: 157 minutes 55.35 seconds (9475.35 seconds total)