Starting phenix.real_space_refine on Wed Sep 17 12:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyw_60581/09_2025/8zyw_60581.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 77 5.16 5 C 5741 2.51 5 N 1469 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8910 Number of models: 1 Model: "" Number of chains: 10 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: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH A 601 " occ=0.76 Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8910 At special positions: 0 Unit cell: (102.6, 98.55, 103.95, 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 77 16.00 O 1623 8.00 N 1469 7.00 C 5741 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: 0.98 Conformation dependent library (CDL) restraints added in 291.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 1 sheets defined 92.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.833A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.084A 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: 3.544A 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: 3.615A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 168 removed outlier: 3.560A 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: 3.543A pdb=" N ALA C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.898A 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: 3.539A 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 26 through 30 removed outlier: 3.733A pdb=" N VAL D 30 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 removed outlier: 4.007A pdb=" N LYS D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 87 removed outlier: 4.095A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 87 " --> pdb=" O MET D 83 " (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: 4.059A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 removed outlier: 3.500A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.121A pdb=" N ILE D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.561A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 50 removed outlier: 3.850A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (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: 3.523A pdb=" N ILE E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.262A 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 197 through 228 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.792A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 removed outlier: 6.561A pdb=" N GLY E 245 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 246 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 248' Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.650A 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 103 through 115 removed outlier: 3.748A pdb=" N GLY F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 168 removed outlier: 3.522A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) 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: 3.768A pdb=" N ALA F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 228 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 250 removed outlier: 4.196A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 249 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 50 Processing helix chain 'G' and resid 51 through 68 removed outlier: 3.728A pdb=" N PHE G 68 " --> pdb=" O LYS G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 3.545A pdb=" N LEU G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 117 through 169 removed outlier: 3.978A pdb=" N VAL G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 196 removed outlier: 3.743A pdb=" N GLY G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) Proline residue: G 177 - end of helix removed outlier: 3.631A pdb=" N VAL G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 228 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.610A pdb=" N LYS G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 250 removed outlier: 3.743A 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 42 810 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2896 1.34 - 1.46: 1813 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 9029 Sorted by residual: bond pdb=" CB ASN C 102 " pdb=" CG ASN C 102 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB MET G 219 " pdb=" CG MET G 219 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG GLN B 49 " pdb=" CD GLN B 49 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB VAL C 142 " pdb=" CG1 VAL C 142 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.54e-01 bond pdb=" CA ASN C 102 " pdb=" CB ASN C 102 " ideal model delta sigma weight residual 1.528 1.542 -0.013 1.66e-02 3.63e+03 6.49e-01 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 12053 2.22 - 4.45: 83 4.45 - 6.67: 16 6.67 - 8.89: 7 8.89 - 11.11: 1 Bond angle restraints: 12160 Sorted by residual: angle pdb=" CA GLN B 49 " pdb=" CB GLN B 49 " pdb=" CG GLN B 49 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA LEU F 112 " pdb=" CB LEU F 112 " pdb=" CG LEU F 112 " ideal model delta sigma weight residual 116.30 127.41 -11.11 3.50e+00 8.16e-02 1.01e+01 angle pdb=" CB MET G 153 " pdb=" CG MET G 153 " pdb=" SD MET G 153 " ideal model delta sigma weight residual 112.70 121.30 -8.60 3.00e+00 1.11e-01 8.23e+00 angle pdb=" N GLN B 49 " pdb=" CA GLN B 49 " pdb=" CB GLN B 49 " ideal model delta sigma weight residual 110.39 114.98 -4.59 1.66e+00 3.63e-01 7.65e+00 angle pdb=" CB MET E 52 " pdb=" CG MET E 52 " pdb=" SD MET E 52 " ideal model delta sigma weight residual 112.70 104.84 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4600 17.60 - 35.20: 598 35.20 - 52.80: 194 52.80 - 70.40: 43 70.40 - 88.00: 8 Dihedral angle restraints: 5443 sinusoidal: 2129 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ASP E 71 " pdb=" CB ASP E 71 " pdb=" CG ASP E 71 " pdb=" OD1 ASP E 71 " ideal model delta sinusoidal sigma weight residual -30.00 -89.12 59.12 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 119 " pdb=" CB ASP C 119 " pdb=" CG ASP C 119 " pdb=" OD1 ASP C 119 " ideal model delta sinusoidal sigma weight residual -30.00 -87.51 57.51 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP E 85 " pdb=" CB ASP E 85 " pdb=" CG ASP E 85 " pdb=" OD1 ASP E 85 " ideal model delta sinusoidal sigma weight residual -30.00 -85.29 55.29 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 5440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1095 0.038 - 0.077: 282 0.077 - 0.115: 63 0.115 - 0.153: 3 0.153 - 0.192: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN B 49 " pdb=" N GLN B 49 " pdb=" C GLN B 49 " pdb=" CB GLN B 49 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CG LEU F 112 " pdb=" CB LEU F 112 " pdb=" CD1 LEU F 112 " pdb=" CD2 LEU F 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1443 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 28 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU B 28 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 28 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 29 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 25 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C LEU B 25 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU B 25 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 26 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 26 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C MET B 26 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B 26 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 27 " -0.010 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 66 2.67 - 3.23: 8730 3.23 - 3.78: 14305 3.78 - 4.34: 17710 4.34 - 4.90: 30708 Nonbonded interactions: 71519 Sorted by model distance: nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.109 3.040 nonbonded pdb=" OG1 THR G 158 " pdb=" OG1 THR G 186 " model vdw 2.201 3.040 nonbonded pdb=" O LEU B 45 " pdb=" NE2 GLN B 49 " model vdw 2.204 3.120 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.218 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG SER A 38 " model vdw 2.303 3.040 ... (remaining 71514 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 250) selection = (chain 'D' and resid 29 through 250) selection = (chain 'E' and resid 29 through 250) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 250)) selection = (chain 'G' and resid 29 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=0.76 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.230 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.032 9029 Z= 0.135 Angle : 0.546 11.114 12160 Z= 0.286 Chirality : 0.037 0.192 1446 Planarity : 0.004 0.040 1543 Dihedral : 17.928 88.000 3305 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.32 % Allowed : 26.81 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.25), residues: 1148 helix: 2.40 (0.16), residues: 992 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.005 0.001 TYR D 237 PHE 0.019 0.001 PHE E 56 TRP 0.010 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9029) covalent geometry : angle 0.54593 (12160) hydrogen bonds : bond 0.11026 ( 810) hydrogen bonds : angle 4.83952 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.325 Fit side-chains REVERT: D 36 LEU cc_start: 0.8892 (tp) cc_final: 0.8607 (tt) REVERT: D 83 MET cc_start: 0.5710 (mmp) cc_final: 0.4761 (tpp) REVERT: E 195 MET cc_start: 0.8676 (mmm) cc_final: 0.8386 (mtm) REVERT: F 169 MET cc_start: 0.8613 (tpp) cc_final: 0.8226 (tpp) REVERT: G 219 MET cc_start: 0.6050 (mmm) cc_final: 0.5741 (mmp) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.1090 time to fit residues: 19.5684 Evaluate side-chains 130 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** G 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.202660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142956 restraints weight = 8948.574| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.30 r_work: 0.3128 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9029 Z= 0.114 Angle : 0.460 8.151 12160 Z= 0.243 Chirality : 0.035 0.159 1446 Planarity : 0.003 0.032 1543 Dihedral : 3.490 33.833 1224 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.49 % Allowed : 26.49 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.25), residues: 1148 helix: 2.79 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 135 TYR 0.005 0.001 TYR D 237 PHE 0.015 0.001 PHE E 56 TRP 0.008 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9029) covalent geometry : angle 0.45959 (12160) hydrogen bonds : bond 0.03843 ( 810) hydrogen bonds : angle 3.58977 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 49 GLN cc_start: 0.6975 (mp10) cc_final: 0.6688 (mp10) REVERT: C 36 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 83 MET cc_start: 0.5519 (mmt) cc_final: 0.5238 (tpt) REVERT: D 36 LEU cc_start: 0.8951 (tp) cc_final: 0.8677 (tt) REVERT: D 68 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: D 219 MET cc_start: 0.6263 (tmm) cc_final: 0.5977 (tmm) REVERT: E 202 ASP cc_start: 0.7522 (m-30) cc_final: 0.7224 (m-30) REVERT: F 153 MET cc_start: 0.9014 (mmm) cc_final: 0.8810 (mmm) REVERT: G 102 ASN cc_start: 0.6932 (OUTLIER) cc_final: 0.6659 (t0) REVERT: G 148 ASP cc_start: 0.7782 (m-30) cc_final: 0.7561 (m-30) outliers start: 14 outliers final: 8 residues processed: 144 average time/residue: 0.0977 time to fit residues: 19.4306 Evaluate side-chains 141 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** D 214 ASN E 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.198659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143240 restraints weight = 8849.818| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.37 r_work: 0.3096 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9029 Z= 0.154 Angle : 0.483 8.564 12160 Z= 0.254 Chirality : 0.037 0.157 1446 Planarity : 0.003 0.035 1543 Dihedral : 3.417 12.304 1221 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.77 % Allowed : 25.74 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.24), residues: 1148 helix: 2.77 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.69 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.005 0.001 TYR F 188 PHE 0.023 0.001 PHE D 44 TRP 0.007 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9029) covalent geometry : angle 0.48298 (12160) hydrogen bonds : bond 0.04112 ( 810) hydrogen bonds : angle 3.57916 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.321 Fit side-chains REVERT: B 49 GLN cc_start: 0.6882 (mp10) cc_final: 0.6573 (mp10) REVERT: D 36 LEU cc_start: 0.8983 (tp) cc_final: 0.8702 (tt) REVERT: D 48 MET cc_start: 0.8608 (tpp) cc_final: 0.8374 (tpp) REVERT: D 56 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: D 68 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: D 219 MET cc_start: 0.6336 (tmm) cc_final: 0.6032 (tmm) REVERT: E 202 ASP cc_start: 0.7571 (m-30) cc_final: 0.7212 (m-30) REVERT: E 244 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: G 148 ASP cc_start: 0.7686 (m-30) cc_final: 0.7388 (m-30) outliers start: 26 outliers final: 14 residues processed: 148 average time/residue: 0.1012 time to fit residues: 20.6837 Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain D residue 56 PHE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** G 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.199277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139238 restraints weight = 9043.339| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.36 r_work: 0.3044 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9029 Z= 0.138 Angle : 0.463 8.543 12160 Z= 0.245 Chirality : 0.036 0.159 1446 Planarity : 0.003 0.038 1543 Dihedral : 3.374 12.613 1221 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.77 % Allowed : 26.17 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.25), residues: 1148 helix: 2.78 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.004 0.001 TYR D 237 PHE 0.017 0.001 PHE D 44 TRP 0.008 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9029) covalent geometry : angle 0.46338 (12160) hydrogen bonds : bond 0.03909 ( 810) hydrogen bonds : angle 3.52229 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: C 173 LYS cc_start: 0.8533 (mttm) cc_final: 0.8188 (mmmm) REVERT: D 36 LEU cc_start: 0.8931 (tp) cc_final: 0.8651 (tt) REVERT: D 48 MET cc_start: 0.8882 (tpp) cc_final: 0.8591 (tpp) REVERT: D 56 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: D 219 MET cc_start: 0.6133 (tmm) cc_final: 0.5851 (tmm) REVERT: E 202 ASP cc_start: 0.7833 (m-30) cc_final: 0.7412 (m-30) REVERT: E 244 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: F 3 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6491 (tt) REVERT: F 20 MET cc_start: 0.2687 (mmt) cc_final: 0.2379 (mmm) REVERT: G 148 ASP cc_start: 0.7811 (m-30) cc_final: 0.7465 (m-30) outliers start: 26 outliers final: 15 residues processed: 150 average time/residue: 0.1001 time to fit residues: 20.7585 Evaluate side-chains 146 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 56 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 55 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 0.0050 chunk 91 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- 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** D 210 GLN G 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.192342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131389 restraints weight = 9028.479| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.70 r_work: 0.2961 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 9029 Z= 0.303 Angle : 0.625 8.263 12160 Z= 0.331 Chirality : 0.043 0.158 1446 Planarity : 0.004 0.040 1543 Dihedral : 3.800 15.221 1221 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.57 % Allowed : 24.89 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.24), residues: 1148 helix: 2.26 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.98 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 208 TYR 0.009 0.001 TYR D 188 PHE 0.019 0.002 PHE A 39 TRP 0.007 0.002 TRP A 18 HIS 0.005 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 9029) covalent geometry : angle 0.62498 (12160) hydrogen bonds : bond 0.05156 ( 810) hydrogen bonds : angle 3.88640 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 49 GLN cc_start: 0.6563 (mp10) cc_final: 0.6307 (mp10) REVERT: C 173 LYS cc_start: 0.8603 (mttm) cc_final: 0.8238 (mmmm) REVERT: C 209 ASP cc_start: 0.6305 (m-30) cc_final: 0.6033 (m-30) REVERT: D 36 LEU cc_start: 0.8969 (tp) cc_final: 0.8637 (tt) REVERT: D 68 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: D 219 MET cc_start: 0.6084 (tmm) cc_final: 0.5392 (tmm) REVERT: E 56 PHE cc_start: 0.8009 (m-80) cc_final: 0.7757 (m-80) REVERT: E 179 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8286 (tpt) REVERT: E 202 ASP cc_start: 0.7864 (m-30) cc_final: 0.7297 (m-30) REVERT: E 244 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: F 3 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6291 (tt) REVERT: F 135 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7848 (mmm-85) REVERT: F 232 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.2348 (ttm110) REVERT: G 72 GLU cc_start: 0.7267 (pm20) cc_final: 0.6987 (pm20) REVERT: G 148 ASP cc_start: 0.8036 (m-30) cc_final: 0.7785 (m-30) REVERT: G 217 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5454 (mp) outliers start: 43 outliers final: 26 residues processed: 167 average time/residue: 0.1048 time to fit residues: 23.8634 Evaluate side-chains 166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.198535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134337 restraints weight = 8841.120| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.88 r_work: 0.3047 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9029 Z= 0.119 Angle : 0.469 8.370 12160 Z= 0.247 Chirality : 0.036 0.160 1446 Planarity : 0.004 0.039 1543 Dihedral : 3.504 18.364 1221 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.19 % Allowed : 26.70 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.25), residues: 1148 helix: 2.72 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -0.84 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 144 TYR 0.005 0.000 TYR D 237 PHE 0.025 0.001 PHE D 44 TRP 0.011 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9029) covalent geometry : angle 0.46874 (12160) hydrogen bonds : bond 0.03896 ( 810) hydrogen bonds : angle 3.57342 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8205 (tmm) cc_final: 0.8001 (tmm) REVERT: C 173 LYS cc_start: 0.8636 (mttm) cc_final: 0.8271 (mmmm) REVERT: D 36 LEU cc_start: 0.8983 (tp) cc_final: 0.8678 (tt) REVERT: D 68 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7306 (m-10) REVERT: D 219 MET cc_start: 0.6245 (tmm) cc_final: 0.5482 (tmm) REVERT: E 56 PHE cc_start: 0.7708 (m-80) cc_final: 0.7458 (m-80) REVERT: E 179 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8102 (tpt) REVERT: E 202 ASP cc_start: 0.7874 (m-30) cc_final: 0.7413 (m-30) REVERT: E 244 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: F 20 MET cc_start: 0.2867 (mmt) cc_final: 0.2550 (mmm) REVERT: F 232 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.2606 (ttm110) REVERT: G 72 GLU cc_start: 0.7322 (pm20) cc_final: 0.7008 (pm20) REVERT: G 148 ASP cc_start: 0.7893 (m-30) cc_final: 0.7375 (m-30) REVERT: G 217 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5500 (mp) outliers start: 30 outliers final: 18 residues processed: 152 average time/residue: 0.1028 time to fit residues: 21.5084 Evaluate side-chains 149 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.203190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142786 restraints weight = 9134.464| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.81 r_work: 0.2972 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9029 Z= 0.231 Angle : 0.562 9.340 12160 Z= 0.295 Chirality : 0.040 0.172 1446 Planarity : 0.004 0.042 1543 Dihedral : 3.673 16.151 1221 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.94 % Allowed : 26.17 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.25), residues: 1148 helix: 2.45 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.94 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 144 TYR 0.007 0.001 TYR F 188 PHE 0.017 0.002 PHE D 44 TRP 0.007 0.002 TRP A 18 HIS 0.004 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 9029) covalent geometry : angle 0.56190 (12160) hydrogen bonds : bond 0.04666 ( 810) hydrogen bonds : angle 3.75564 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8251 (tmm) cc_final: 0.8038 (tmm) REVERT: B 49 GLN cc_start: 0.6601 (mp10) cc_final: 0.6096 (mp10) REVERT: C 56 PHE cc_start: 0.7427 (m-80) cc_final: 0.7142 (m-80) REVERT: C 173 LYS cc_start: 0.8546 (mttm) cc_final: 0.8184 (mmmm) REVERT: C 209 ASP cc_start: 0.6286 (m-30) cc_final: 0.5993 (m-30) REVERT: D 36 LEU cc_start: 0.8915 (tp) cc_final: 0.8590 (tt) REVERT: D 48 MET cc_start: 0.8796 (tpp) cc_final: 0.8550 (mpp) REVERT: D 68 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: D 219 MET cc_start: 0.6155 (tmm) cc_final: 0.5861 (tmm) REVERT: E 56 PHE cc_start: 0.7959 (m-80) cc_final: 0.7637 (m-80) REVERT: E 179 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (tpt) REVERT: E 202 ASP cc_start: 0.7863 (m-30) cc_final: 0.7298 (m-30) REVERT: E 244 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6045 (tt0) REVERT: F 20 MET cc_start: 0.2790 (mmt) cc_final: 0.2494 (mmm) REVERT: F 232 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.2404 (ttm110) REVERT: G 148 ASP cc_start: 0.7967 (m-30) cc_final: 0.7681 (m-30) REVERT: G 217 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5383 (mp) outliers start: 37 outliers final: 26 residues processed: 162 average time/residue: 0.0988 time to fit residues: 22.2550 Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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** D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.206709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144511 restraints weight = 9010.088| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.66 r_work: 0.3056 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9029 Z= 0.138 Angle : 0.487 9.303 12160 Z= 0.255 Chirality : 0.037 0.165 1446 Planarity : 0.004 0.042 1543 Dihedral : 3.513 14.893 1221 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.30 % Allowed : 27.23 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.25), residues: 1148 helix: 2.65 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.90 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.005 0.001 TYR D 237 PHE 0.019 0.001 PHE D 56 TRP 0.010 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9029) covalent geometry : angle 0.48689 (12160) hydrogen bonds : bond 0.03980 ( 810) hydrogen bonds : angle 3.59080 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8212 (tmm) cc_final: 0.7934 (tmm) REVERT: B 49 GLN cc_start: 0.6681 (mp10) cc_final: 0.6112 (mp10) REVERT: C 173 LYS cc_start: 0.8509 (mttm) cc_final: 0.8134 (mmmm) REVERT: D 36 LEU cc_start: 0.8983 (tp) cc_final: 0.8672 (tt) REVERT: D 68 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: D 179 MET cc_start: 0.8519 (mmm) cc_final: 0.8089 (tpt) REVERT: D 219 MET cc_start: 0.6362 (tmm) cc_final: 0.5566 (tmm) REVERT: E 52 MET cc_start: 0.7535 (tpp) cc_final: 0.6998 (tpt) REVERT: E 56 PHE cc_start: 0.7799 (m-80) cc_final: 0.7341 (m-80) REVERT: E 179 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8293 (tpt) REVERT: E 202 ASP cc_start: 0.7801 (m-30) cc_final: 0.7355 (m-30) REVERT: E 244 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5932 (tt0) REVERT: F 20 MET cc_start: 0.2836 (mmt) cc_final: 0.2527 (mmm) REVERT: F 105 MET cc_start: 0.6761 (ttm) cc_final: 0.6418 (ttm) REVERT: F 232 ARG cc_start: 0.4552 (OUTLIER) cc_final: 0.2453 (ttm110) REVERT: G 72 GLU cc_start: 0.7348 (pm20) cc_final: 0.7135 (pm20) REVERT: G 148 ASP cc_start: 0.7865 (m-30) cc_final: 0.7315 (m-30) REVERT: G 217 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5525 (mp) outliers start: 31 outliers final: 23 residues processed: 155 average time/residue: 0.0981 time to fit residues: 21.1846 Evaluate side-chains 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 28 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- 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** D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.205339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142926 restraints weight = 9126.192| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.59 r_work: 0.3018 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9029 Z= 0.170 Angle : 0.518 8.858 12160 Z= 0.271 Chirality : 0.038 0.166 1446 Planarity : 0.004 0.042 1543 Dihedral : 3.558 14.544 1221 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.72 % Allowed : 26.91 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.24), residues: 1148 helix: 2.58 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -0.93 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 135 TYR 0.005 0.001 TYR G 188 PHE 0.027 0.002 PHE D 56 TRP 0.009 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9029) covalent geometry : angle 0.51831 (12160) hydrogen bonds : bond 0.04206 ( 810) hydrogen bonds : angle 3.63898 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 173 LYS cc_start: 0.8507 (mttm) cc_final: 0.8127 (mmmm) REVERT: D 36 LEU cc_start: 0.8992 (tp) cc_final: 0.8683 (tt) REVERT: D 68 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: D 219 MET cc_start: 0.6418 (tmm) cc_final: 0.5617 (tmm) REVERT: E 56 PHE cc_start: 0.7845 (m-80) cc_final: 0.7491 (m-80) REVERT: E 179 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8406 (tpt) REVERT: E 202 ASP cc_start: 0.7860 (m-30) cc_final: 0.7408 (m-30) REVERT: E 244 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: F 20 MET cc_start: 0.2876 (mmt) cc_final: 0.2562 (mmm) REVERT: F 105 MET cc_start: 0.6763 (ttm) cc_final: 0.6425 (ttm) REVERT: F 232 ARG cc_start: 0.4572 (OUTLIER) cc_final: 0.2733 (mmp-170) REVERT: G 72 GLU cc_start: 0.7382 (pm20) cc_final: 0.7163 (pm20) REVERT: G 148 ASP cc_start: 0.7904 (m-30) cc_final: 0.7356 (m-30) REVERT: G 217 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5614 (mp) outliers start: 35 outliers final: 27 residues processed: 163 average time/residue: 0.0938 time to fit residues: 21.2583 Evaluate side-chains 165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.198690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137325 restraints weight = 8883.648| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.43 r_work: 0.3062 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9029 Z= 0.123 Angle : 0.488 9.052 12160 Z= 0.256 Chirality : 0.036 0.165 1446 Planarity : 0.004 0.042 1543 Dihedral : 3.447 14.229 1221 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.98 % Allowed : 27.55 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.24), residues: 1148 helix: 2.79 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 144 TYR 0.005 0.001 TYR D 237 PHE 0.036 0.001 PHE D 56 TRP 0.011 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9029) covalent geometry : angle 0.48826 (12160) hydrogen bonds : bond 0.03831 ( 810) hydrogen bonds : angle 3.56467 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8410 (tmm) cc_final: 0.7858 (tmm) REVERT: B 49 GLN cc_start: 0.6764 (mp10) cc_final: 0.6376 (mp10) REVERT: C 52 MET cc_start: 0.7661 (tpp) cc_final: 0.6955 (mtm) REVERT: C 173 LYS cc_start: 0.8482 (mttm) cc_final: 0.8105 (mmmm) REVERT: D 36 LEU cc_start: 0.8916 (tp) cc_final: 0.8653 (tt) REVERT: D 68 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: D 219 MET cc_start: 0.6367 (tmm) cc_final: 0.5578 (tmm) REVERT: E 56 PHE cc_start: 0.7861 (m-80) cc_final: 0.7469 (m-80) REVERT: E 202 ASP cc_start: 0.7857 (m-30) cc_final: 0.7407 (m-30) REVERT: E 244 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: F 20 MET cc_start: 0.2806 (mmt) cc_final: 0.2499 (mmm) REVERT: F 105 MET cc_start: 0.6749 (ttm) cc_final: 0.6400 (ttm) REVERT: F 232 ARG cc_start: 0.4507 (OUTLIER) cc_final: 0.2703 (mmp-170) REVERT: G 72 GLU cc_start: 0.7330 (pm20) cc_final: 0.7114 (pm20) REVERT: G 148 ASP cc_start: 0.7908 (m-30) cc_final: 0.7434 (m-30) REVERT: G 217 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5497 (mp) outliers start: 28 outliers final: 21 residues processed: 157 average time/residue: 0.0952 time to fit residues: 20.7065 Evaluate side-chains 156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.209164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147032 restraints weight = 8910.863| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.02 r_work: 0.3106 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9029 Z= 0.117 Angle : 0.506 9.099 12160 Z= 0.257 Chirality : 0.036 0.166 1446 Planarity : 0.004 0.041 1543 Dihedral : 3.402 14.300 1221 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.55 % Allowed : 27.98 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.24), residues: 1148 helix: 2.86 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 144 TYR 0.006 0.001 TYR D 188 PHE 0.035 0.001 PHE D 56 TRP 0.009 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9029) covalent geometry : angle 0.50609 (12160) hydrogen bonds : bond 0.03736 ( 810) hydrogen bonds : angle 3.53781 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.11 seconds wall clock time: 38 minutes 5.09 seconds (2285.09 seconds total)