Starting phenix.real_space_refine on Tue Aug 4 20:36:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vv0_65371/08_2026/9vv0_65371.map" } resolution = 2.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.048 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 41 5.16 5 C 4150 2.51 5 N 1103 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6553 At special positions: 0 Unit cell: (100.225, 99.17, 84.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1259 8.00 N 1103 7.00 C 4150 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA2-3 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 354.0 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.6% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.664A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.912A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.741A pdb=" N ARG B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.153A pdb=" N MET C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.809A pdb=" N ARG C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'E' and resid 201 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.564A pdb=" N SER C 162 " --> pdb=" O ASN A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.564A pdb=" N SER C 162 " --> pdb=" O ASN A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.469A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.816A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.957A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.957A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.615A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.833A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.293A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 498 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: 0.97 Time building geometry restraints manager: 0.89 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: 2112 1.34 - 1.46: 1192 1.46 - 1.57: 3343 1.57 - 1.69: 1 1.69 - 1.81: 68 Bond restraints: 6716 Sorted by residual: bond pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU A 157 " pdb=" CG GLU A 157 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.93e-01 bond pdb=" C LYS A 242 " pdb=" O LYS A 242 " ideal model delta sigma weight residual 1.246 1.239 0.007 9.20e-03 1.18e+04 5.21e-01 bond pdb=" CB THR A 276 " pdb=" CG2 THR A 276 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 bond pdb=" CB GLU A 30 " pdb=" CG GLU A 30 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.48e-01 ... (remaining 6711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 8852 1.20 - 2.41: 224 2.41 - 3.61: 64 3.61 - 4.82: 10 4.82 - 6.02: 4 Bond angle restraints: 9154 Sorted by residual: angle pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.70e+00 3.46e-01 1.22e+01 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.07e+00 angle pdb=" CA GLU A 30 " pdb=" CB GLU A 30 " pdb=" CG GLU A 30 " ideal model delta sigma weight residual 114.10 118.89 -4.79 2.00e+00 2.50e-01 5.73e+00 angle pdb=" CB GLU A 157 " pdb=" CG GLU A 157 " pdb=" CD GLU A 157 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.05e+00 angle pdb=" CA GLU A 157 " pdb=" CB GLU A 157 " pdb=" CG GLU A 157 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 3753 22.14 - 44.29: 270 44.29 - 66.43: 48 66.43 - 88.57: 12 88.57 - 110.72: 10 Dihedral angle restraints: 4093 sinusoidal: 1693 harmonic: 2400 Sorted by residual: dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual 54.75 -55.97 110.72 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O4 MAN F 4 " ideal model delta sinusoidal sigma weight residual 176.13 65.94 110.19 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C5 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O3 MAN F 4 " ideal model delta sinusoidal sigma weight residual -174.53 -65.13 -109.40 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 4090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 787 0.044 - 0.089: 197 0.089 - 0.133: 70 0.133 - 0.178: 0 0.178 - 0.222: 1 Chirality restraints: 1055 Sorted by residual: chirality pdb=" C2 SIA G 2 " pdb=" O3 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.41 -0.09 2.00e-02 2.50e+03 1.96e+01 chirality pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" O3 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.41 2.18 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.76 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1052 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 123 " 0.007 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE C 123 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 123 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 123 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 123 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 123 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 123 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 157 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" CD GLU A 157 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A 157 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 157 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 30 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" CD GLU A 30 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 30 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 30 " 0.008 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 3202 2.97 - 3.45: 6073 3.45 - 3.93: 11214 3.93 - 4.42: 13530 4.42 - 4.90: 21110 Nonbonded interactions: 55129 Sorted by model distance: nonbonded pdb=" N GLU A 19 " pdb=" OE1 GLU A 19 " model vdw 2.482 3.120 nonbonded pdb=" O5 BMA F 3 " pdb=" O6 BMA F 3 " model vdw 2.508 2.432 nonbonded pdb=" N ASP C 220 " pdb=" OD1 ASP C 220 " model vdw 2.531 3.120 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.542 3.120 nonbonded pdb=" C3 GAL G 1 " pdb=" O6 SIA G 2 " model vdw 2.550 2.776 ... (remaining 55124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6722 Z= 0.150 Angle : 0.522 6.022 9172 Z= 0.266 Chirality : 0.043 0.222 1055 Planarity : 0.004 0.027 1171 Dihedral : 16.564 110.716 2543 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.54 % Allowed : 17.76 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 819 helix: -1.72 (0.65), residues: 61 sheet: 0.74 (0.37), residues: 191 loop : -0.23 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.008 0.001 TYR D 36 PHE 0.025 0.001 PHE C 123 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6716) covalent geometry : angle 0.51514 / 0.26 ( 9154) hydrogen bonds : bond 0.14562 / 8.76 ( 171) hydrogen bonds : angle 6.93463 / 4.76 ( 498) link_ALPHA1-3 : bond 0.00369 / 0.19 ( 1) link_ALPHA1-3 : angle 3.37801 / 1.73 ( 3) link_ALPHA1-6 : bond 0.00666 / 0.35 ( 1) link_ALPHA1-6 : angle 1.50243 / 0.84 ( 3) link_BETA1-4 : bond 0.00221 / 0.11 ( 2) link_BETA1-4 : angle 1.94146 / 1.00 ( 6) link_BETA1-6 : bond 0.00101 / 0.05 ( 1) link_BETA1-6 : angle 1.51235 / 0.74 ( 3) link_BETA2-3 : bond 0.00208 / 0.11 ( 1) link_BETA2-3 : angle 1.05185 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.174 Fit side-chains REVERT: A 44 GLN cc_start: 0.9461 (mt0) cc_final: 0.9222 (tt0) REVERT: A 193 TYR cc_start: 0.9394 (m-80) cc_final: 0.8807 (m-80) REVERT: A 220 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9025 (mp) REVERT: B 67 ARG cc_start: 0.8981 (mtp180) cc_final: 0.8605 (mtp-110) REVERT: B 97 GLN cc_start: 0.9072 (mt0) cc_final: 0.8791 (mt0) REVERT: C 145 GLU cc_start: 0.8746 (pm20) cc_final: 0.8356 (pm20) REVERT: E 201 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8902 (pp) REVERT: E 205 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7552 (ppp-140) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.5411 time to fit residues: 77.9818 Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 44 GLN A 158 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 55 GLN B 111 GLN B 206 GLN B 240 ASN C 160 GLN C 235 GLN E 200 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.072952 restraints weight = 10130.420| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.31 r_work: 0.2791 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6722 Z= 0.085 Angle : 0.470 7.761 9172 Z= 0.234 Chirality : 0.042 0.185 1055 Planarity : 0.003 0.027 1171 Dihedral : 8.986 89.754 1071 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.78 % Allowed : 15.94 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 819 helix: -1.57 (0.66), residues: 61 sheet: 0.61 (0.36), residues: 201 loop : -0.11 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.006 0.001 TYR B 31 PHE 0.013 0.001 PHE A 100 TRP 0.006 0.001 TRP A 249 HIS 0.003 0.000 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 ( 6716) covalent geometry : angle 0.46389 / 0.23 ( 9154) hydrogen bonds : bond 0.02838 / 1.85 ( 171) hydrogen bonds : angle 5.58726 / 3.84 ( 498) link_ALPHA1-3 : bond 0.00639 / 0.34 ( 1) link_ALPHA1-3 : angle 2.69267 / 1.42 ( 3) link_ALPHA1-6 : bond 0.00604 / 0.32 ( 1) link_ALPHA1-6 : angle 1.44099 / 0.80 ( 3) link_BETA1-4 : bond 0.00289 / 0.15 ( 2) link_BETA1-4 : angle 1.96358 / 1.05 ( 6) link_BETA1-6 : bond 0.00529 / 0.28 ( 1) link_BETA1-6 : angle 1.02748 / 0.52 ( 3) link_BETA2-3 : bond 0.00319 / 0.17 ( 1) link_BETA2-3 : angle 0.97861 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.153 Fit side-chains REVERT: A 44 GLN cc_start: 0.9452 (mt0) cc_final: 0.9246 (tt0) REVERT: A 65 ARG cc_start: 0.8776 (mmt90) cc_final: 0.7229 (mtp180) REVERT: A 193 TYR cc_start: 0.9279 (m-80) cc_final: 0.8688 (m-80) REVERT: A 220 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8976 (mp) REVERT: B 67 ARG cc_start: 0.8985 (mtp180) cc_final: 0.8606 (mtp-110) REVERT: B 97 GLN cc_start: 0.9079 (mt0) cc_final: 0.8786 (mt0) REVERT: C 145 GLU cc_start: 0.8782 (pm20) cc_final: 0.8352 (pm20) REVERT: D 42 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8664 (mttp) REVERT: E 201 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8939 (pp) REVERT: E 205 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7363 (ppp-140) outliers start: 27 outliers final: 7 residues processed: 152 average time/residue: 0.4763 time to fit residues: 75.8475 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.074070 restraints weight = 10157.495| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.31 r_work: 0.2816 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6722 Z= 0.078 Angle : 0.453 5.531 9172 Z= 0.228 Chirality : 0.041 0.175 1055 Planarity : 0.003 0.027 1171 Dihedral : 7.478 87.788 1066 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.50 % Allowed : 16.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.29), residues: 819 helix: -1.53 (0.65), residues: 61 sheet: 0.62 (0.36), residues: 201 loop : -0.05 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.007 0.001 TYR D 36 PHE 0.009 0.001 PHE C 215 TRP 0.005 0.001 TRP C 155 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 ( 6716) covalent geometry : angle 0.44424 / 0.23 ( 9154) hydrogen bonds : bond 0.02703 / 1.76 ( 171) hydrogen bonds : angle 5.32428 / 3.67 ( 498) link_ALPHA1-3 : bond 0.00189 / 0.10 ( 1) link_ALPHA1-3 : angle 3.53373 / 1.86 ( 3) link_ALPHA1-6 : bond 0.00478 / 0.25 ( 1) link_ALPHA1-6 : angle 1.45490 / 0.80 ( 3) link_BETA1-4 : bond 0.00235 / 0.12 ( 2) link_BETA1-4 : angle 2.06022 / 1.05 ( 6) link_BETA1-6 : bond 0.00411 / 0.22 ( 1) link_BETA1-6 : angle 1.24574 / 0.63 ( 3) link_BETA2-3 : bond 0.00404 / 0.21 ( 1) link_BETA2-3 : angle 0.86716 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.142 Fit side-chains REVERT: A 44 GLN cc_start: 0.9431 (mt0) cc_final: 0.9212 (tt0) REVERT: A 65 ARG cc_start: 0.8559 (mmt90) cc_final: 0.7321 (mtp180) REVERT: A 193 TYR cc_start: 0.9229 (m-80) cc_final: 0.8735 (m-10) REVERT: A 220 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9027 (mp) REVERT: B 67 ARG cc_start: 0.8985 (mtp180) cc_final: 0.8602 (mtp-110) REVERT: B 97 GLN cc_start: 0.9014 (mt0) cc_final: 0.8681 (mt0) REVERT: C 145 GLU cc_start: 0.8768 (pm20) cc_final: 0.8385 (pm20) REVERT: C 148 MET cc_start: 0.8323 (ppp) cc_final: 0.8087 (ptm) REVERT: E 201 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8957 (pp) REVERT: E 205 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7733 (ppp-140) outliers start: 25 outliers final: 8 residues processed: 150 average time/residue: 0.4670 time to fit residues: 73.3648 Evaluate side-chains 145 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 0.0170 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN C 101 ASN C 179 ASN E 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.073656 restraints weight = 10164.581| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.30 r_work: 0.2807 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6722 Z= 0.096 Angle : 0.467 5.007 9172 Z= 0.233 Chirality : 0.041 0.194 1055 Planarity : 0.003 0.029 1171 Dihedral : 7.539 86.338 1065 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 16.78 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 819 helix: -1.81 (0.59), residues: 68 sheet: 0.65 (0.36), residues: 200 loop : -0.02 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.008 0.001 TYR D 36 PHE 0.009 0.001 PHE C 215 TRP 0.004 0.001 TRP C 155 HIS 0.001 0.000 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6716) covalent geometry : angle 0.45872 / 0.23 ( 9154) hydrogen bonds : bond 0.02599 / 1.72 ( 171) hydrogen bonds : angle 5.22424 / 3.60 ( 498) link_ALPHA1-3 : bond 0.00276 / 0.15 ( 1) link_ALPHA1-3 : angle 3.27224 / 1.69 ( 3) link_ALPHA1-6 : bond 0.00456 / 0.24 ( 1) link_ALPHA1-6 : angle 1.52165 / 0.85 ( 3) link_BETA1-4 : bond 0.00341 / 0.18 ( 2) link_BETA1-4 : angle 2.02261 / 1.08 ( 6) link_BETA1-6 : bond 0.00003 / 0.00 ( 1) link_BETA1-6 : angle 1.70346 / 0.83 ( 3) link_BETA2-3 : bond 0.00273 / 0.14 ( 1) link_BETA2-3 : angle 0.86746 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.144 Fit side-chains REVERT: A 44 GLN cc_start: 0.9436 (mt0) cc_final: 0.9228 (tt0) REVERT: A 65 ARG cc_start: 0.8538 (mmt90) cc_final: 0.7321 (mtp180) REVERT: A 193 TYR cc_start: 0.9240 (m-80) cc_final: 0.8759 (m-10) REVERT: A 208 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8044 (mt) REVERT: B 67 ARG cc_start: 0.8997 (mtp180) cc_final: 0.8728 (mtp-110) REVERT: B 97 GLN cc_start: 0.9052 (mt0) cc_final: 0.8744 (mt0) REVERT: B 151 ARG cc_start: 0.8491 (mmp80) cc_final: 0.8127 (tpt90) REVERT: C 68 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8738 (ptt-90) REVERT: C 145 GLU cc_start: 0.8740 (pm20) cc_final: 0.8350 (pm20) REVERT: C 148 MET cc_start: 0.8306 (ppp) cc_final: 0.8088 (ptm) REVERT: E 205 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7746 (ppp-140) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 0.4788 time to fit residues: 71.9185 Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN E 200 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.086300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068903 restraints weight = 10421.544| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.32 r_work: 0.2719 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 6722 Z= 0.280 Angle : 0.555 5.965 9172 Z= 0.280 Chirality : 0.045 0.213 1055 Planarity : 0.004 0.031 1171 Dihedral : 7.629 87.517 1061 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.08 % Allowed : 17.48 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.29), residues: 819 helix: -1.62 (0.63), residues: 61 sheet: 0.69 (0.36), residues: 199 loop : -0.12 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 104 TYR 0.013 0.002 TYR D 36 PHE 0.018 0.002 PHE C 123 TRP 0.006 0.001 TRP A 163 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.28 ( 6716) covalent geometry : angle 0.54815 / 0.28 ( 9154) hydrogen bonds : bond 0.03324 / 2.22 ( 171) hydrogen bonds : angle 5.57392 / 3.85 ( 498) link_ALPHA1-3 : bond 0.00099 / 0.05 ( 1) link_ALPHA1-3 : angle 3.33266 / 1.70 ( 3) link_ALPHA1-6 : bond 0.00495 / 0.26 ( 1) link_ALPHA1-6 : angle 1.58251 / 0.88 ( 3) link_BETA1-4 : bond 0.00027 / 0.01 ( 2) link_BETA1-4 : angle 1.92770 / 0.98 ( 6) link_BETA1-6 : bond 0.00048 / 0.03 ( 1) link_BETA1-6 : angle 1.58044 / 0.79 ( 3) link_BETA2-3 : bond 0.00311 / 0.16 ( 1) link_BETA2-3 : angle 1.21629 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.231 Fit side-chains REVERT: A 193 TYR cc_start: 0.9346 (m-80) cc_final: 0.8711 (m-80) REVERT: A 208 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.7907 (mt) REVERT: A 220 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9106 (mp) REVERT: B 67 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8636 (mtp-110) REVERT: B 97 GLN cc_start: 0.9063 (mt0) cc_final: 0.8765 (mt0) REVERT: C 68 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8886 (ptt-90) REVERT: C 145 GLU cc_start: 0.8777 (pm20) cc_final: 0.8386 (pm20) REVERT: E 205 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.7569 (ppp-140) REVERT: E 207 ASN cc_start: 0.7906 (t0) cc_final: 0.7603 (t0) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 0.4398 time to fit residues: 63.7434 Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 0.0270 chunk 67 optimal weight: 0.0060 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN E 200 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071706 restraints weight = 10328.416| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.33 r_work: 0.2768 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6722 Z= 0.101 Angle : 0.489 5.293 9172 Z= 0.245 Chirality : 0.042 0.200 1055 Planarity : 0.003 0.030 1171 Dihedral : 7.466 86.727 1061 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.80 % Allowed : 17.48 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.29), residues: 819 helix: -1.49 (0.64), residues: 61 sheet: 0.66 (0.36), residues: 199 loop : -0.06 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.008 0.001 TYR A 193 PHE 0.015 0.001 PHE C 123 TRP 0.005 0.001 TRP A 249 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6716) covalent geometry : angle 0.48098 / 0.24 ( 9154) hydrogen bonds : bond 0.02730 / 1.82 ( 171) hydrogen bonds : angle 5.36717 / 3.70 ( 498) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-3 : angle 3.46817 / 1.79 ( 3) link_ALPHA1-6 : bond 0.00486 / 0.26 ( 1) link_ALPHA1-6 : angle 1.51423 / 0.84 ( 3) link_BETA1-4 : bond 0.00334 / 0.17 ( 2) link_BETA1-4 : angle 1.97188 / 1.07 ( 6) link_BETA1-6 : bond 0.00017 / 0.01 ( 1) link_BETA1-6 : angle 1.61260 / 0.78 ( 3) link_BETA2-3 : bond 0.00348 / 0.18 ( 1) link_BETA2-3 : angle 0.92580 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.183 Fit side-chains REVERT: A 65 ARG cc_start: 0.8629 (mmt90) cc_final: 0.7028 (mtp180) REVERT: A 193 TYR cc_start: 0.9302 (m-80) cc_final: 0.8736 (m-80) REVERT: A 208 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 67 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8653 (mtp-110) REVERT: B 97 GLN cc_start: 0.9037 (mt0) cc_final: 0.8726 (mt0) REVERT: C 68 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8862 (ptt-90) REVERT: C 145 GLU cc_start: 0.8740 (pm20) cc_final: 0.8358 (pm20) REVERT: D 42 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8638 (mttp) REVERT: E 205 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.7705 (ppp-140) outliers start: 20 outliers final: 12 residues processed: 141 average time/residue: 0.4545 time to fit residues: 67.1566 Evaluate side-chains 145 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071590 restraints weight = 10106.581| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.30 r_work: 0.2770 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6722 Z= 0.117 Angle : 0.494 5.087 9172 Z= 0.246 Chirality : 0.042 0.203 1055 Planarity : 0.003 0.030 1171 Dihedral : 7.513 86.195 1061 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.08 % Allowed : 17.20 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.29), residues: 819 helix: -1.44 (0.64), residues: 61 sheet: 0.66 (0.36), residues: 198 loop : -0.04 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 67 TYR 0.008 0.001 TYR A 193 PHE 0.013 0.001 PHE C 123 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.000 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6716) covalent geometry : angle 0.48534 / 0.24 ( 9154) hydrogen bonds : bond 0.02728 / 1.82 ( 171) hydrogen bonds : angle 5.25475 / 3.63 ( 498) link_ALPHA1-3 : bond 0.00258 / 0.14 ( 1) link_ALPHA1-3 : angle 3.36973 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00484 / 0.25 ( 1) link_ALPHA1-6 : angle 1.49852 / 0.83 ( 3) link_BETA1-4 : bond 0.00258 / 0.13 ( 2) link_BETA1-4 : angle 2.06668 / 1.12 ( 6) link_BETA1-6 : bond 0.00133 / 0.07 ( 1) link_BETA1-6 : angle 1.72667 / 0.84 ( 3) link_BETA2-3 : bond 0.00320 / 0.17 ( 1) link_BETA2-3 : angle 0.91928 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.162 Fit side-chains REVERT: A 65 ARG cc_start: 0.8835 (mmt90) cc_final: 0.7259 (mtp180) REVERT: A 193 TYR cc_start: 0.9296 (m-80) cc_final: 0.8711 (m-80) REVERT: A 208 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8271 (mt) REVERT: A 220 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9063 (mp) REVERT: B 67 ARG cc_start: 0.9025 (mtp180) cc_final: 0.8677 (mtp-110) REVERT: B 97 GLN cc_start: 0.9030 (mt0) cc_final: 0.8719 (mt0) REVERT: C 68 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8825 (ptt-90) REVERT: C 145 GLU cc_start: 0.8739 (pm20) cc_final: 0.8290 (pm20) REVERT: D 42 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8649 (mttp) REVERT: E 201 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8991 (pp) REVERT: E 205 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8164 (ppp-140) outliers start: 22 outliers final: 10 residues processed: 141 average time/residue: 0.4680 time to fit residues: 69.0272 Evaluate side-chains 144 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 240 ASN E 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.070461 restraints weight = 10239.126| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.31 r_work: 0.2748 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6722 Z= 0.168 Angle : 0.515 5.896 9172 Z= 0.257 Chirality : 0.043 0.205 1055 Planarity : 0.003 0.028 1171 Dihedral : 7.567 86.183 1061 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 17.62 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 819 helix: -1.45 (0.64), residues: 61 sheet: 0.66 (0.36), residues: 199 loop : -0.09 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.009 0.001 TYR D 36 PHE 0.012 0.001 PHE C 123 TRP 0.004 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6716) covalent geometry : angle 0.50789 / 0.26 ( 9154) hydrogen bonds : bond 0.02944 / 1.98 ( 171) hydrogen bonds : angle 5.33218 / 3.69 ( 498) link_ALPHA1-3 : bond 0.00214 / 0.11 ( 1) link_ALPHA1-3 : angle 3.35861 / 1.73 ( 3) link_ALPHA1-6 : bond 0.00471 / 0.25 ( 1) link_ALPHA1-6 : angle 1.49439 / 0.83 ( 3) link_BETA1-4 : bond 0.00205 / 0.11 ( 2) link_BETA1-4 : angle 1.99627 / 1.07 ( 6) link_BETA1-6 : bond 0.00022 / 0.01 ( 1) link_BETA1-6 : angle 1.58081 / 0.77 ( 3) link_BETA2-3 : bond 0.00212 / 0.11 ( 1) link_BETA2-3 : angle 0.99219 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.185 Fit side-chains REVERT: A 65 ARG cc_start: 0.8754 (mmt90) cc_final: 0.6988 (mtp180) REVERT: A 193 TYR cc_start: 0.9317 (m-80) cc_final: 0.8761 (m-80) REVERT: A 208 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.7972 (mt) REVERT: A 220 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9078 (mp) REVERT: B 67 ARG cc_start: 0.9013 (mtp180) cc_final: 0.8639 (mtp-110) REVERT: B 97 GLN cc_start: 0.9045 (mt0) cc_final: 0.8735 (mt0) REVERT: B 150 GLU cc_start: 0.8763 (pp20) cc_final: 0.8557 (pp20) REVERT: C 68 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8844 (ptt-90) REVERT: C 145 GLU cc_start: 0.8742 (pm20) cc_final: 0.8335 (pm20) REVERT: D 42 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8649 (mttp) REVERT: E 201 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8982 (pp) REVERT: E 205 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.7700 (ppp-140) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 0.4592 time to fit residues: 67.2252 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 240 ASN E 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.070898 restraints weight = 10215.365| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.31 r_work: 0.2757 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6722 Z= 0.132 Angle : 0.511 6.143 9172 Z= 0.253 Chirality : 0.042 0.204 1055 Planarity : 0.003 0.028 1171 Dihedral : 7.541 85.856 1061 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.66 % Allowed : 17.90 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.29), residues: 819 helix: -1.41 (0.64), residues: 61 sheet: 0.65 (0.36), residues: 198 loop : -0.05 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 104 TYR 0.008 0.001 TYR A 193 PHE 0.012 0.001 PHE C 123 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6716) covalent geometry : angle 0.50295 / 0.25 ( 9154) hydrogen bonds : bond 0.02810 / 1.89 ( 171) hydrogen bonds : angle 5.33687 / 3.68 ( 498) link_ALPHA1-3 : bond 0.00262 / 0.14 ( 1) link_ALPHA1-3 : angle 3.37446 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00502 / 0.26 ( 1) link_ALPHA1-6 : angle 1.49120 / 0.83 ( 3) link_BETA1-4 : bond 0.00252 / 0.13 ( 2) link_BETA1-4 : angle 2.02732 / 1.10 ( 6) link_BETA1-6 : bond 0.00026 / 0.01 ( 1) link_BETA1-6 : angle 1.57182 / 0.77 ( 3) link_BETA2-3 : bond 0.00337 / 0.18 ( 1) link_BETA2-3 : angle 0.97108 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.248 Fit side-chains REVERT: A 65 ARG cc_start: 0.8861 (mmt90) cc_final: 0.7181 (mtp180) REVERT: A 193 TYR cc_start: 0.9313 (m-80) cc_final: 0.8748 (m-80) REVERT: A 208 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 220 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9088 (mp) REVERT: B 67 ARG cc_start: 0.9020 (mtp180) cc_final: 0.8677 (mtp-110) REVERT: B 97 GLN cc_start: 0.9039 (mt0) cc_final: 0.8723 (mt0) REVERT: B 150 GLU cc_start: 0.8759 (pp20) cc_final: 0.8554 (pp20) REVERT: C 68 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8840 (ptt-90) REVERT: C 145 GLU cc_start: 0.8698 (pm20) cc_final: 0.8311 (pm20) REVERT: C 227 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9164 (ttp) REVERT: D 42 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8646 (mttp) REVERT: E 201 LEU cc_start: 0.9247 (pp) cc_final: 0.9029 (pp) REVERT: E 205 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8256 (ppp-140) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.4648 time to fit residues: 64.2768 Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 240 ASN E 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.070960 restraints weight = 10210.165| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.31 r_work: 0.2759 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6722 Z= 0.136 Angle : 0.506 6.094 9172 Z= 0.252 Chirality : 0.042 0.202 1055 Planarity : 0.003 0.028 1171 Dihedral : 7.369 85.522 1061 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 17.76 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.29), residues: 819 helix: -1.38 (0.64), residues: 61 sheet: 0.66 (0.36), residues: 198 loop : -0.06 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.008 0.001 TYR D 36 PHE 0.011 0.001 PHE C 123 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6716) covalent geometry : angle 0.49906 / 0.25 ( 9154) hydrogen bonds : bond 0.02810 / 1.89 ( 171) hydrogen bonds : angle 5.27345 / 3.65 ( 498) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-3 : angle 3.34676 / 1.72 ( 3) link_ALPHA1-6 : bond 0.00513 / 0.27 ( 1) link_ALPHA1-6 : angle 1.48835 / 0.83 ( 3) link_BETA1-4 : bond 0.00274 / 0.14 ( 2) link_BETA1-4 : angle 1.95122 / 1.05 ( 6) link_BETA1-6 : bond 0.00110 / 0.06 ( 1) link_BETA1-6 : angle 1.44030 / 0.71 ( 3) link_BETA2-3 : bond 0.00308 / 0.16 ( 1) link_BETA2-3 : angle 0.97613 / 0.51 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.147 Fit side-chains REVERT: A 193 TYR cc_start: 0.9306 (m-80) cc_final: 0.8751 (m-80) REVERT: A 220 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9098 (mp) REVERT: B 67 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8661 (mtp-110) REVERT: B 97 GLN cc_start: 0.9041 (mt0) cc_final: 0.8724 (mt0) REVERT: B 150 GLU cc_start: 0.8762 (pp20) cc_final: 0.8561 (pp20) REVERT: C 68 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8830 (ptt-90) REVERT: C 145 GLU cc_start: 0.8719 (pm20) cc_final: 0.8337 (pm20) REVERT: D 42 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8652 (mttp) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.4387 time to fit residues: 61.2588 Evaluate side-chains 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 205 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.0000 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 240 ASN E 200 ASN E 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.070785 restraints weight = 10185.759| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.31 r_work: 0.2755 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6722 Z= 0.153 Angle : 0.522 7.398 9172 Z= 0.262 Chirality : 0.043 0.202 1055 Planarity : 0.003 0.028 1171 Dihedral : 7.383 85.442 1061 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 17.76 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 819 helix: -1.39 (0.64), residues: 61 sheet: 0.66 (0.36), residues: 199 loop : -0.09 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.008 0.001 TYR D 36 PHE 0.011 0.001 PHE C 123 TRP 0.004 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6716) covalent geometry : angle 0.51482 / 0.26 ( 9154) hydrogen bonds : bond 0.02885 / 1.94 ( 171) hydrogen bonds : angle 5.27759 / 3.65 ( 498) link_ALPHA1-3 : bond 0.00222 / 0.12 ( 1) link_ALPHA1-3 : angle 3.34973 / 1.72 ( 3) link_ALPHA1-6 : bond 0.00434 / 0.23 ( 1) link_ALPHA1-6 : angle 1.46034 / 0.81 ( 3) link_BETA1-4 : bond 0.00220 / 0.11 ( 2) link_BETA1-4 : angle 1.94168 / 1.03 ( 6) link_BETA1-6 : bond 0.00092 / 0.05 ( 1) link_BETA1-6 : angle 1.50295 / 0.74 ( 3) link_BETA2-3 : bond 0.00353 / 0.19 ( 1) link_BETA2-3 : angle 1.01199 / 0.53 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.16 seconds wall clock time: 44 minutes 44.17 seconds (2684.17 seconds total)