Starting phenix.real_space_refine on Thu Mar 13 06:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyz_60584/03_2025/8zyz_60584.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 78 5.16 5 Na 2 4.78 5 C 5745 2.51 5 N 1471 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 368 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 1606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1616 Chain: "D" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1621 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.71 Number of scatterers: 8918 At special positions: 0 Unit cell: (102.6, 98.55, 106.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 Na 2 11.00 O 1622 8.00 N 1471 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 91.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.820A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.943A pdb=" N PHE B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'C' and resid 31 through 50 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.548A pdb=" N PHE C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.512A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 168 removed outlier: 3.500A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.623A pdb=" N ALA C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.609A pdb=" N GLU C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 85 removed outlier: 3.989A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 117 through 167 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 175 through 196 removed outlier: 3.771A pdb=" N VAL D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.067A pdb=" N ILE D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.523A pdb=" N ARG D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 50 removed outlier: 3.795A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 removed outlier: 3.552A pdb=" N ILE E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 196 through 228 Processing helix chain 'E' and resid 230 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.536A pdb=" N VAL F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 68 Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 102 through 115 Processing helix chain 'F' and resid 117 through 167 Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 195 removed outlier: 3.734A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 227 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.700A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 50 Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 72 through 87 Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.610A pdb=" N ASP G 114 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 169 Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 196 removed outlier: 3.565A pdb=" N GLY G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) Proline residue: G 177 - end of helix Processing helix chain 'G' and resid 196 through 228 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.937A pdb=" N ASN G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.791A pdb=" N ARG G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 812 hydrogen bonds defined for protein. 2411 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: 2.44 Time building geometry restraints manager: 2.72 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: 2896 1.34 - 1.46: 1892 1.46 - 1.59: 4093 1.59 - 1.71: 0 1.71 - 1.83: 154 Bond restraints: 9035 Sorted by residual: bond pdb=" CB MET C 179 " pdb=" CG MET C 179 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB ASN G 243 " pdb=" CG ASN G 243 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB MET D 179 " pdb=" CG MET D 179 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB THR C 158 " pdb=" CG2 THR C 158 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.30e-01 bond pdb=" CB ILE C 61 " pdb=" CG2 ILE C 61 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.86e-01 ... (remaining 9030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12099 2.58 - 5.17: 62 5.17 - 7.75: 6 7.75 - 10.34: 1 10.34 - 12.92: 1 Bond angle restraints: 12169 Sorted by residual: angle pdb=" CB MET G 83 " pdb=" CG MET G 83 " pdb=" SD MET G 83 " ideal model delta sigma weight residual 112.70 125.62 -12.92 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CG MET G 83 " pdb=" SD MET G 83 " pdb=" CE MET G 83 " ideal model delta sigma weight residual 100.90 106.34 -5.44 2.20e+00 2.07e-01 6.12e+00 angle pdb=" CB MET F 52 " pdb=" CG MET F 52 " pdb=" SD MET F 52 " ideal model delta sigma weight residual 112.70 120.06 -7.36 3.00e+00 1.11e-01 6.02e+00 angle pdb=" C ASP E 148 " pdb=" N VAL E 149 " pdb=" CA VAL E 149 " ideal model delta sigma weight residual 121.55 118.18 3.37 1.42e+00 4.96e-01 5.63e+00 angle pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " ideal model delta sigma weight residual 112.70 105.71 6.99 3.00e+00 1.11e-01 5.43e+00 ... (remaining 12164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4577 17.90 - 35.79: 655 35.79 - 53.69: 175 53.69 - 71.59: 32 71.59 - 89.48: 11 Dihedral angle restraints: 5450 sinusoidal: 2132 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ASP D 133 " pdb=" CB ASP D 133 " pdb=" CG ASP D 133 " pdb=" OD1 ASP D 133 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU C 211 " pdb=" CG GLU C 211 " pdb=" CD GLU C 211 " pdb=" OE1 GLU C 211 " ideal model delta sinusoidal sigma weight residual 0.00 -89.48 89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP F 31 " pdb=" CB ASP F 31 " pdb=" CG ASP F 31 " pdb=" OD1 ASP F 31 " ideal model delta sinusoidal sigma weight residual -30.00 -85.55 55.55 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 909 0.029 - 0.059: 370 0.059 - 0.088: 119 0.088 - 0.118: 44 0.118 - 0.147: 5 Chirality restraints: 1447 Sorted by residual: chirality pdb=" CA ASP E 148 " pdb=" N ASP E 148 " pdb=" C ASP E 148 " pdb=" CB ASP E 148 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ASN G 243 " pdb=" N ASN G 243 " pdb=" C ASN G 243 " pdb=" CB ASN G 243 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA PRO D 151 " pdb=" N PRO D 151 " pdb=" C PRO D 151 " pdb=" CB PRO D 151 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1444 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 243 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C ASN G 243 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN G 243 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU G 244 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 148 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" CG ASP C 148 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP C 148 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 148 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 15 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 16 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " -0.023 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 50 2.65 - 3.21: 8360 3.21 - 3.77: 14464 3.77 - 4.34: 18178 4.34 - 4.90: 31349 Nonbonded interactions: 72401 Sorted by model distance: nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.087 3.040 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.146 3.040 nonbonded pdb=" O ASN G 243 " pdb=" ND2 ASN G 243 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP E 31 " pdb=" OH TYR E 188 " model vdw 2.166 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG SER A 38 " model vdw 2.201 3.040 ... (remaining 72396 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 59) } ncs_group { reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 250)) selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 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: 0.150 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.820 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 0.039 9035 Z= 0.223 Angle : 0.530 12.923 12169 Z= 0.271 Chirality : 0.037 0.147 1447 Planarity : 0.004 0.042 1544 Dihedral : 18.051 89.484 3310 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.11 % Allowed : 29.12 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.25), residues: 1149 helix: 2.52 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.18 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 18 HIS 0.004 0.001 HIS E 136 PHE 0.014 0.002 PHE E 143 TYR 0.008 0.001 TYR D 241 ARG 0.009 0.001 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.851 Fit side-chains REVERT: B 30 MET cc_start: 0.8053 (ttt) cc_final: 0.7768 (ttm) REVERT: E 75 ASP cc_start: 0.8422 (m-30) cc_final: 0.7674 (t70) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.1841 time to fit residues: 33.1510 Evaluate side-chains 127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 243 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.183249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121343 restraints weight = 10321.647| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.93 r_work: 0.3032 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9035 Z= 0.197 Angle : 0.478 7.584 12169 Z= 0.248 Chirality : 0.036 0.122 1447 Planarity : 0.004 0.042 1544 Dihedral : 3.441 13.392 1225 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.38 % Allowed : 26.67 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.25), residues: 1149 helix: 2.73 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.18 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 PHE 0.018 0.001 PHE A 39 TYR 0.006 0.001 TYR D 241 ARG 0.003 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.975 Fit side-chains REVERT: C 56 PHE cc_start: 0.7115 (m-10) cc_final: 0.6737 (m-80) REVERT: C 67 MET cc_start: 0.7702 (ptt) cc_final: 0.7181 (ptp) REVERT: C 239 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7190 (mtpp) REVERT: E 75 ASP cc_start: 0.8560 (m-30) cc_final: 0.7518 (t70) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.1756 time to fit residues: 35.3374 Evaluate side-chains 131 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.185344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134248 restraints weight = 15430.207| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.83 r_work: 0.3126 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9035 Z= 0.146 Angle : 0.438 7.653 12169 Z= 0.228 Chirality : 0.035 0.114 1447 Planarity : 0.003 0.041 1544 Dihedral : 3.312 13.071 1223 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.38 % Allowed : 26.89 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.25), residues: 1149 helix: 2.97 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -0.16 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS E 136 PHE 0.015 0.001 PHE A 39 TYR 0.004 0.001 TYR G 241 ARG 0.004 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.075 Fit side-chains REVERT: C 67 MET cc_start: 0.7724 (ptt) cc_final: 0.7182 (ptp) REVERT: C 239 LYS cc_start: 0.7310 (mtpp) cc_final: 0.7051 (mtpp) REVERT: E 75 ASP cc_start: 0.8563 (m-30) cc_final: 0.7560 (t70) REVERT: F 148 ASP cc_start: 0.8598 (m-30) cc_final: 0.8245 (m-30) REVERT: F 207 ARG cc_start: 0.8964 (tpt-90) cc_final: 0.8634 (tpp80) REVERT: G 135 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7358 (mtp180) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.1772 time to fit residues: 36.4163 Evaluate side-chains 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.180229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.119541 restraints weight = 10348.149| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.82 r_work: 0.2972 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9035 Z= 0.284 Angle : 0.524 7.453 12169 Z= 0.271 Chirality : 0.039 0.133 1447 Planarity : 0.004 0.045 1544 Dihedral : 3.566 13.367 1223 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.44 % Allowed : 25.61 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.25), residues: 1149 helix: 2.65 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -0.24 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 18 HIS 0.005 0.001 HIS D 136 PHE 0.019 0.002 PHE F 44 TYR 0.008 0.001 TYR D 241 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 56 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: C 67 MET cc_start: 0.7742 (ptt) cc_final: 0.7164 (ptp) REVERT: C 239 LYS cc_start: 0.7382 (mtpp) cc_final: 0.7146 (mtpp) REVERT: E 67 MET cc_start: 0.7403 (mmt) cc_final: 0.7156 (ttm) REVERT: G 83 MET cc_start: 0.5180 (mmp) cc_final: 0.4785 (mmm) REVERT: G 135 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7060 (mtp180) outliers start: 23 outliers final: 20 residues processed: 144 average time/residue: 0.1877 time to fit residues: 38.9179 Evaluate side-chains 146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.183462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127938 restraints weight = 11631.610| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.46 r_work: 0.3107 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.169 Angle : 0.448 6.182 12169 Z= 0.235 Chirality : 0.036 0.126 1447 Planarity : 0.004 0.042 1544 Dihedral : 3.396 12.655 1223 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.44 % Allowed : 26.14 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.25), residues: 1149 helix: 2.87 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.26 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.019 0.001 PHE A 32 TYR 0.006 0.001 TYR F 188 ARG 0.003 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.948 Fit side-chains REVERT: B 56 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6744 (m-10) REVERT: C 56 PHE cc_start: 0.7464 (m-10) cc_final: 0.7110 (m-80) REVERT: C 67 MET cc_start: 0.7150 (ptt) cc_final: 0.6566 (ptp) REVERT: D 179 MET cc_start: 0.8012 (tpp) cc_final: 0.7616 (ttt) REVERT: E 67 MET cc_start: 0.7572 (mmt) cc_final: 0.7262 (ttm) REVERT: E 75 ASP cc_start: 0.8581 (m-30) cc_final: 0.7569 (t70) REVERT: F 148 ASP cc_start: 0.8522 (m-30) cc_final: 0.8097 (m-30) REVERT: G 83 MET cc_start: 0.5030 (mmp) cc_final: 0.4718 (mmm) REVERT: G 135 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7350 (mtp180) outliers start: 23 outliers final: 14 residues processed: 151 average time/residue: 0.1910 time to fit residues: 41.7884 Evaluate side-chains 144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.185249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134267 restraints weight = 15400.431| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.86 r_work: 0.3126 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9035 Z= 0.148 Angle : 0.449 7.797 12169 Z= 0.232 Chirality : 0.035 0.126 1447 Planarity : 0.003 0.041 1544 Dihedral : 3.334 13.104 1223 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.81 % Allowed : 26.99 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.25), residues: 1149 helix: 3.06 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -0.12 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS C 136 PHE 0.033 0.001 PHE A 32 TYR 0.004 0.001 TYR F 188 ARG 0.003 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.009 Fit side-chains REVERT: B 56 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: C 56 PHE cc_start: 0.7293 (m-10) cc_final: 0.6954 (m-80) REVERT: C 67 MET cc_start: 0.7304 (ptt) cc_final: 0.6706 (ptp) REVERT: C 179 MET cc_start: 0.7826 (mtt) cc_final: 0.7519 (mtt) REVERT: E 67 MET cc_start: 0.7498 (mmt) cc_final: 0.7176 (ttm) REVERT: E 75 ASP cc_start: 0.8500 (m-30) cc_final: 0.7568 (t70) REVERT: F 148 ASP cc_start: 0.8503 (m-30) cc_final: 0.8079 (m-30) REVERT: G 83 MET cc_start: 0.4939 (mmp) cc_final: 0.4659 (mmm) REVERT: G 135 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7302 (mtp180) outliers start: 17 outliers final: 13 residues processed: 141 average time/residue: 0.1819 time to fit residues: 37.2551 Evaluate side-chains 143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.184710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123107 restraints weight = 10655.294| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.84 r_work: 0.3062 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9035 Z= 0.156 Angle : 0.448 8.186 12169 Z= 0.233 Chirality : 0.036 0.126 1447 Planarity : 0.003 0.043 1544 Dihedral : 3.323 12.413 1223 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 27.63 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.24), residues: 1149 helix: 3.11 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.19 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 18 HIS 0.002 0.001 HIS D 136 PHE 0.015 0.001 PHE A 39 TYR 0.004 0.001 TYR F 188 ARG 0.004 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.043 Fit side-chains REVERT: B 56 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: C 56 PHE cc_start: 0.7084 (m-10) cc_final: 0.6755 (m-80) REVERT: C 67 MET cc_start: 0.7280 (ptt) cc_final: 0.6646 (ptp) REVERT: E 67 MET cc_start: 0.7389 (mmt) cc_final: 0.7186 (ttm) REVERT: E 75 ASP cc_start: 0.8419 (m-30) cc_final: 0.7475 (t70) REVERT: F 148 ASP cc_start: 0.8449 (m-30) cc_final: 0.7960 (m-30) REVERT: G 76 LEU cc_start: 0.7434 (mm) cc_final: 0.7162 (mm) REVERT: G 83 MET cc_start: 0.4898 (mmp) cc_final: 0.4611 (mmm) REVERT: G 135 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7103 (mtp180) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.1835 time to fit residues: 37.7235 Evaluate side-chains 145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.185571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124165 restraints weight = 12316.963| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.08 r_work: 0.3051 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9035 Z= 0.148 Angle : 0.440 8.447 12169 Z= 0.229 Chirality : 0.035 0.128 1447 Planarity : 0.003 0.043 1544 Dihedral : 3.304 12.944 1223 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 27.21 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.24), residues: 1149 helix: 3.17 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.015 0.001 PHE A 39 TYR 0.004 0.001 TYR F 188 ARG 0.007 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.950 Fit side-chains REVERT: B 56 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: C 56 PHE cc_start: 0.7166 (m-10) cc_final: 0.6803 (m-80) REVERT: C 67 MET cc_start: 0.7298 (ptt) cc_final: 0.6669 (ptp) REVERT: E 67 MET cc_start: 0.7432 (mmt) cc_final: 0.7219 (ttm) REVERT: E 75 ASP cc_start: 0.8316 (m-30) cc_final: 0.7420 (t70) REVERT: F 148 ASP cc_start: 0.8465 (m-30) cc_final: 0.7977 (m-30) REVERT: G 76 LEU cc_start: 0.7386 (mm) cc_final: 0.7064 (mm) REVERT: G 83 MET cc_start: 0.4856 (mmp) cc_final: 0.4614 (mmm) REVERT: G 135 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7129 (mtp180) outliers start: 20 outliers final: 16 residues processed: 146 average time/residue: 0.1789 time to fit residues: 38.0040 Evaluate side-chains 151 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.0670 chunk 79 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.186609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133985 restraints weight = 12265.890| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.55 r_work: 0.3164 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9035 Z= 0.137 Angle : 0.436 8.768 12169 Z= 0.227 Chirality : 0.035 0.119 1447 Planarity : 0.003 0.043 1544 Dihedral : 3.246 12.995 1223 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.81 % Allowed : 27.52 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.24), residues: 1149 helix: 3.28 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.15 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.001 0.001 HIS D 136 PHE 0.017 0.001 PHE A 33 TYR 0.004 0.001 TYR F 188 ARG 0.005 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7650 (t80) cc_final: 0.7439 (t80) REVERT: B 56 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6717 (m-10) REVERT: C 56 PHE cc_start: 0.7276 (m-10) cc_final: 0.6947 (m-80) REVERT: C 69 LYS cc_start: 0.8131 (mttp) cc_final: 0.7280 (ttpt) REVERT: E 67 MET cc_start: 0.7600 (mmt) cc_final: 0.7283 (ttm) REVERT: E 75 ASP cc_start: 0.8374 (m-30) cc_final: 0.7485 (t70) REVERT: E 148 ASP cc_start: 0.8273 (m-30) cc_final: 0.8008 (m-30) REVERT: F 148 ASP cc_start: 0.8382 (m-30) cc_final: 0.7938 (m-30) REVERT: G 76 LEU cc_start: 0.7508 (mm) cc_final: 0.7173 (mm) REVERT: G 83 MET cc_start: 0.4866 (mmp) cc_final: 0.4595 (mmm) REVERT: G 135 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7293 (mtp180) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.1912 time to fit residues: 39.9721 Evaluate side-chains 146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.185788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134189 restraints weight = 15447.777| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.84 r_work: 0.3134 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9035 Z= 0.146 Angle : 0.439 8.616 12169 Z= 0.229 Chirality : 0.035 0.118 1447 Planarity : 0.003 0.043 1544 Dihedral : 3.261 13.157 1223 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 27.63 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.24), residues: 1149 helix: 3.22 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -0.16 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 18 HIS 0.002 0.001 HIS D 136 PHE 0.026 0.001 PHE A 32 TYR 0.007 0.001 TYR F 188 ARG 0.008 0.000 ARG G 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.237 Fit side-chains REVERT: B 56 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: C 56 PHE cc_start: 0.7200 (m-10) cc_final: 0.6942 (m-80) REVERT: C 67 MET cc_start: 0.7329 (ptt) cc_final: 0.6846 (ptp) REVERT: C 69 LYS cc_start: 0.8136 (mttp) cc_final: 0.7371 (ttpt) REVERT: E 75 ASP cc_start: 0.8385 (m-30) cc_final: 0.7509 (t70) REVERT: E 148 ASP cc_start: 0.8051 (m-30) cc_final: 0.7819 (m-30) REVERT: F 148 ASP cc_start: 0.8293 (m-30) cc_final: 0.7835 (m-30) REVERT: G 76 LEU cc_start: 0.7574 (mm) cc_final: 0.7233 (mm) REVERT: G 83 MET cc_start: 0.4892 (mmp) cc_final: 0.4668 (mmm) REVERT: G 135 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7278 (mtp180) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 0.2182 time to fit residues: 46.2156 Evaluate side-chains 151 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 237 TYR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.184562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149772 restraints weight = 18557.848| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.85 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.179 Angle : 0.463 9.212 12169 Z= 0.242 Chirality : 0.036 0.120 1447 Planarity : 0.004 0.044 1544 Dihedral : 3.340 13.276 1223 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.81 % Allowed : 27.63 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.24), residues: 1149 helix: 3.11 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.24 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 18 HIS 0.002 0.001 HIS D 136 PHE 0.033 0.001 PHE A 32 TYR 0.010 0.001 TYR F 188 ARG 0.011 0.000 ARG G 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.61 seconds wall clock time: 91 minutes 55.10 seconds (5515.10 seconds total)