Starting phenix.real_space_refine on Thu Mar 13 06:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyw_60581/03_2025/8zyw_60581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyw_60581/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyw_60581/03_2025/8zyw_60581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyw_60581/03_2025/8zyw_60581.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyw_60581/03_2025/8zyw_60581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyw_60581/03_2025/8zyw_60581.cif" } resolution = 3.43 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= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.82, per 1000 atoms: 0.65 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: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.76 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: 2.48 Time building geometry restraints manager: 2.89 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: 0.000 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.510 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- 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= 0.189 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 (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: 3.05 (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 TRP 0.010 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.019 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 : 0.889 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: 0.2273 time to fit residues: 40.6248 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 : 0.890 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 40.0000 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.209571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148830 restraints weight = 8865.326| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.15 r_work: 0.3107 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9029 Z= 0.182 Angle : 0.473 8.208 12160 Z= 0.250 Chirality : 0.036 0.163 1446 Planarity : 0.003 0.033 1543 Dihedral : 3.537 34.114 1224 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (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: 3.55 (0.25), residues: 1148 helix: 2.73 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -0.61 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.015 0.001 PHE E 56 TYR 0.004 0.001 TYR D 237 ARG 0.003 0.000 ARG D 135 *********************** 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 147 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.003 Fit side-chains REVERT: B 49 GLN cc_start: 0.6781 (mp10) cc_final: 0.6518 (mp10) REVERT: C 36 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 83 MET cc_start: 0.5605 (mmt) cc_final: 0.5209 (tpt) REVERT: D 36 LEU cc_start: 0.8935 (tp) cc_final: 0.8663 (tt) REVERT: D 68 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: D 219 MET cc_start: 0.6040 (tmm) cc_final: 0.5534 (tmm) REVERT: E 179 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8439 (tpt) REVERT: E 202 ASP cc_start: 0.7526 (m-30) cc_final: 0.7197 (m-30) REVERT: F 153 MET cc_start: 0.9020 (mmm) cc_final: 0.8801 (mmm) REVERT: G 105 MET cc_start: 0.5964 (ttp) cc_final: 0.5686 (ttp) REVERT: G 148 ASP cc_start: 0.7684 (m-30) cc_final: 0.7442 (m-30) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.2272 time to fit residues: 44.2295 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU 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 179 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 30 VAL 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 25 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.200429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138684 restraints weight = 8913.672| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.84 r_work: 0.3098 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0957 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= 0.179 Angle : 0.450 8.754 12160 Z= 0.236 Chirality : 0.036 0.161 1446 Planarity : 0.003 0.034 1543 Dihedral : 3.325 12.364 1221 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 (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: 3.71 (0.24), residues: 1148 helix: 2.86 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.012 0.001 PHE A 39 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.012 Fit side-chains REVERT: B 49 GLN cc_start: 0.6785 (mp10) cc_final: 0.6448 (mp10) REVERT: C 36 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 36 LEU cc_start: 0.8939 (tp) cc_final: 0.8667 (tt) REVERT: D 56 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7343 (m-10) REVERT: D 68 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: D 219 MET cc_start: 0.6141 (tmm) cc_final: 0.5580 (tmm) REVERT: E 202 ASP cc_start: 0.7597 (m-30) cc_final: 0.7240 (m-30) REVERT: E 244 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: F 20 MET cc_start: 0.2756 (mmt) cc_final: 0.2322 (mmm) REVERT: G 102 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6684 (t0) REVERT: G 148 ASP cc_start: 0.7759 (m-30) cc_final: 0.7473 (m-30) outliers start: 26 outliers final: 14 residues processed: 150 average time/residue: 0.2085 time to fit residues: 43.2699 Evaluate side-chains 148 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 165 MET Chi-restraints excluded: chain D residue 56 PHE 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 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 102 ASN Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE 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 32 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.209702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145630 restraints weight = 9016.094| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.20 r_work: 0.3077 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9029 Z= 0.215 Angle : 0.467 8.520 12160 Z= 0.246 Chirality : 0.036 0.159 1446 Planarity : 0.003 0.037 1543 Dihedral : 3.339 12.356 1221 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 (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: 3.71 (0.24), residues: 1148 helix: 2.84 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.59 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 PHE 0.012 0.001 PHE D 143 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 : 1.017 Fit side-chains revert: symmetry clash REVERT: D 36 LEU cc_start: 0.8965 (tp) cc_final: 0.8691 (tt) REVERT: D 56 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: D 219 MET cc_start: 0.6111 (tmm) cc_final: 0.5837 (tmm) REVERT: E 202 ASP cc_start: 0.7775 (m-30) cc_final: 0.7364 (m-30) REVERT: E 244 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: F 3 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6529 (tt) REVERT: F 20 MET cc_start: 0.2760 (mmt) cc_final: 0.2439 (mmm) REVERT: G 148 ASP cc_start: 0.7763 (m-30) cc_final: 0.7424 (m-30) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.2193 time to fit residues: 45.2571 Evaluate side-chains 149 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 165 MET 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 149 VAL 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 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 200 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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** C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.211718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149723 restraints weight = 8899.530| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.50 r_work: 0.3097 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1251 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= 0.168 Angle : 0.446 8.351 12160 Z= 0.234 Chirality : 0.035 0.161 1446 Planarity : 0.003 0.039 1543 Dihedral : 3.271 12.703 1221 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.77 % Allowed : 26.49 % Favored : 70.74 % 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: 3.92 (0.24), residues: 1148 helix: 3.00 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.53 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.012 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8165 (tmm) cc_final: 0.7959 (tmm) REVERT: B 49 GLN cc_start: 0.6518 (mp10) cc_final: 0.6243 (mp10) REVERT: D 36 LEU cc_start: 0.8916 (tp) cc_final: 0.8657 (tt) REVERT: D 56 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: D 68 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7049 (m-10) REVERT: D 219 MET cc_start: 0.6082 (tmm) cc_final: 0.5833 (tmm) REVERT: E 52 MET cc_start: 0.7497 (tpp) cc_final: 0.7221 (tpt) REVERT: E 202 ASP cc_start: 0.7849 (m-30) cc_final: 0.7500 (m-30) REVERT: E 244 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: F 3 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6648 (tt) REVERT: F 20 MET cc_start: 0.2827 (mmt) cc_final: 0.2519 (mmm) REVERT: G 72 GLU cc_start: 0.7280 (pm20) cc_final: 0.7040 (pm20) REVERT: G 148 ASP cc_start: 0.7790 (m-30) cc_final: 0.7426 (m-30) REVERT: G 217 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5561 (mp) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.2453 time to fit residues: 51.2062 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 : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 56 PHE 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 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR 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 Chi-restraints excluded: chain G residue 200 ILE 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 24 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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** C 243 ASN G 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.201340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140740 restraints weight = 8834.885| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.24 r_work: 0.3108 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9029 Z= 0.150 Angle : 0.436 9.605 12160 Z= 0.227 Chirality : 0.035 0.170 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.208 12.920 1221 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.87 % Allowed : 26.38 % Favored : 70.74 % 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: 4.04 (0.25), residues: 1148 helix: 3.05 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.014 0.001 PHE E 56 TYR 0.005 0.000 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8055 (tmm) cc_final: 0.7806 (tmm) REVERT: B 49 GLN cc_start: 0.6435 (mp10) cc_final: 0.6145 (mp10) REVERT: D 36 LEU cc_start: 0.8883 (tp) cc_final: 0.8638 (tt) REVERT: D 56 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: D 68 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: D 219 MET cc_start: 0.5997 (tmm) cc_final: 0.5750 (tmm) REVERT: E 52 MET cc_start: 0.7419 (tpp) cc_final: 0.7136 (tpt) REVERT: E 202 ASP cc_start: 0.7819 (m-30) cc_final: 0.7470 (m-30) REVERT: E 244 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6221 (tt0) REVERT: F 3 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6432 (tt) REVERT: F 20 MET cc_start: 0.2774 (mmt) cc_final: 0.2476 (mmm) REVERT: G 28 MET cc_start: 0.4010 (tpp) cc_final: 0.3728 (tpp) REVERT: G 72 GLU cc_start: 0.7268 (pm20) cc_final: 0.7064 (pm20) REVERT: G 105 MET cc_start: 0.6021 (ttp) cc_final: 0.5792 (tmm) REVERT: G 217 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5493 (mp) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 0.2064 time to fit residues: 43.7849 Evaluate side-chains 151 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 165 MET Chi-restraints excluded: chain D residue 56 PHE 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 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 149 VAL 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 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 200 ILE Chi-restraints excluded: chain G residue 217 LEU 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 73 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 0.0010 chunk 11 optimal weight: 0.0670 chunk 91 optimal weight: 9.9990 overall best weight: 0.9928 ------------------------------------------------------------------------------- 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** C 243 ASN G 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.211939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149808 restraints weight = 9039.897| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.83 r_work: 0.3121 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 0.032 9029 Z= 0.170 Angle : 0.447 8.739 12160 Z= 0.234 Chirality : 0.035 0.167 1446 Planarity : 0.003 0.041 1543 Dihedral : 3.209 12.824 1221 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.30 % Allowed : 25.85 % Favored : 70.85 % 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: 4.02 (0.25), residues: 1148 helix: 3.02 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.47 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.015 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** 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 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8075 (tmm) cc_final: 0.7794 (tmm) REVERT: B 49 GLN cc_start: 0.6386 (mp10) cc_final: 0.6093 (mp10) REVERT: D 36 LEU cc_start: 0.8888 (tp) cc_final: 0.8632 (tt) REVERT: D 56 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.7086 (m-10) REVERT: D 68 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: D 83 MET cc_start: 0.5810 (mmp) cc_final: 0.5083 (tpp) REVERT: D 179 MET cc_start: 0.8363 (mmm) cc_final: 0.8020 (tpt) REVERT: D 219 MET cc_start: 0.6000 (tmm) cc_final: 0.5754 (tmm) REVERT: E 49 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8077 (ttmm) REVERT: E 52 MET cc_start: 0.7485 (tpp) cc_final: 0.7161 (tpt) REVERT: E 202 ASP cc_start: 0.7820 (m-30) cc_final: 0.7479 (m-30) REVERT: E 244 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: F 3 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6530 (tt) REVERT: F 20 MET cc_start: 0.2962 (mmt) cc_final: 0.2718 (mmm) REVERT: F 232 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.2664 (mtt90) REVERT: G 105 MET cc_start: 0.6277 (ttp) cc_final: 0.5904 (ttp) REVERT: G 217 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5473 (mp) outliers start: 31 outliers final: 22 residues processed: 158 average time/residue: 0.2824 time to fit residues: 61.2711 Evaluate side-chains 160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 165 MET Chi-restraints excluded: chain D residue 56 PHE 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 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 149 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 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 200 ILE 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 58 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** C 243 ASN D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.210335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147411 restraints weight = 9130.829| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.88 r_work: 0.3071 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9029 Z= 0.210 Angle : 0.474 8.693 12160 Z= 0.249 Chirality : 0.036 0.163 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.297 12.561 1221 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.51 % Allowed : 25.64 % Favored : 70.85 % 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: 3.85 (0.25), residues: 1148 helix: 2.89 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -0.50 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.019 0.001 PHE D 44 TYR 0.004 0.001 TYR D 237 ARG 0.005 0.000 ARG D 135 *********************** 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 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8101 (tmm) cc_final: 0.7816 (tmm) REVERT: B 49 GLN cc_start: 0.6393 (mp10) cc_final: 0.6069 (mp10) REVERT: D 36 LEU cc_start: 0.8909 (tp) cc_final: 0.8636 (tt) REVERT: D 68 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7417 (m-10) REVERT: D 179 MET cc_start: 0.8489 (mmm) cc_final: 0.8170 (tpt) REVERT: D 219 MET cc_start: 0.6011 (tmm) cc_final: 0.5751 (tmm) REVERT: E 49 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8097 (ttmm) REVERT: E 52 MET cc_start: 0.7474 (tpp) cc_final: 0.7134 (tpt) REVERT: E 202 ASP cc_start: 0.7867 (m-30) cc_final: 0.7504 (m-30) REVERT: E 244 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: F 3 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6441 (tt) REVERT: F 20 MET cc_start: 0.2992 (mmt) cc_final: 0.2750 (mmm) REVERT: F 232 ARG cc_start: 0.4447 (OUTLIER) cc_final: 0.2455 (mtt90) REVERT: G 28 MET cc_start: 0.3841 (tpp) cc_final: 0.3572 (tpp) REVERT: G 72 GLU cc_start: 0.7216 (pm20) cc_final: 0.7000 (pm20) REVERT: G 105 MET cc_start: 0.6226 (ttp) cc_final: 0.5922 (tmm) REVERT: G 217 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5552 (mp) outliers start: 33 outliers final: 23 residues processed: 164 average time/residue: 0.2703 time to fit residues: 59.5572 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 165 MET 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 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 120 VAL Chi-restraints excluded: chain F residue 149 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 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 242 LEU 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 200 ILE 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 35 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.206438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145155 restraints weight = 8991.820| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.46 r_work: 0.3044 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1596 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= 0.266 Angle : 0.504 8.559 12160 Z= 0.265 Chirality : 0.038 0.166 1446 Planarity : 0.004 0.040 1543 Dihedral : 3.421 13.670 1221 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.19 % Allowed : 26.17 % Favored : 70.64 % 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: 3.65 (0.25), residues: 1148 helix: 2.78 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.57 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS E 136 PHE 0.026 0.002 PHE D 56 TYR 0.006 0.001 TYR G 188 ARG 0.006 0.000 ARG D 135 *********************** 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 165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8114 (tmm) cc_final: 0.7831 (tmm) REVERT: B 49 GLN cc_start: 0.6505 (mp10) cc_final: 0.6177 (mp10) REVERT: D 36 LEU cc_start: 0.8954 (tp) cc_final: 0.8683 (tt) REVERT: D 67 MET cc_start: 0.7915 (tmm) cc_final: 0.7573 (tmm) REVERT: D 68 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: D 179 MET cc_start: 0.8589 (mmm) cc_final: 0.8235 (tpt) REVERT: D 210 GLN cc_start: 0.7052 (mt0) cc_final: 0.6841 (mt0) REVERT: D 219 MET cc_start: 0.6118 (tmm) cc_final: 0.5818 (tmm) REVERT: E 52 MET cc_start: 0.7491 (tpp) cc_final: 0.7204 (tpt) REVERT: E 202 ASP cc_start: 0.7845 (m-30) cc_final: 0.7459 (m-30) REVERT: E 244 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5992 (tt0) REVERT: F 3 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6508 (tt) REVERT: F 20 MET cc_start: 0.2811 (mmt) cc_final: 0.2508 (mmm) REVERT: F 232 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.2895 (mmp-170) REVERT: G 72 GLU cc_start: 0.7187 (pm20) cc_final: 0.6951 (pm20) REVERT: G 105 MET cc_start: 0.6272 (ttp) cc_final: 0.5871 (ttp) REVERT: G 148 ASP cc_start: 0.7714 (m-30) cc_final: 0.7242 (m-30) REVERT: G 217 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5448 (mp) outliers start: 30 outliers final: 22 residues processed: 158 average time/residue: 0.2136 time to fit residues: 46.9783 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 165 MET 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 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 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 F residue 242 LEU 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 192 LEU Chi-restraints excluded: chain G residue 200 ILE 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 0 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.8182 ------------------------------------------------------------------------------- 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** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.206679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143437 restraints weight = 8996.561| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.57 r_work: 0.3053 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9029 Z= 0.251 Angle : 0.501 8.627 12160 Z= 0.264 Chirality : 0.038 0.186 1446 Planarity : 0.004 0.039 1543 Dihedral : 3.434 14.011 1221 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.98 % Allowed : 26.60 % Favored : 70.43 % 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: 3.65 (0.24), residues: 1148 helix: 2.77 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.47 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 PHE 0.031 0.002 PHE D 56 TYR 0.005 0.001 TYR G 188 ARG 0.005 0.000 ARG D 135 ********************** 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 161 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8185 (tmm) cc_final: 0.7888 (tmm) REVERT: B 49 GLN cc_start: 0.6545 (mp10) cc_final: 0.6208 (mp10) REVERT: C 173 LYS cc_start: 0.8621 (mttt) cc_final: 0.8362 (mtpt) REVERT: D 36 LEU cc_start: 0.8968 (tp) cc_final: 0.8681 (tt) REVERT: D 48 MET cc_start: 0.8886 (tpp) cc_final: 0.8625 (tpp) REVERT: D 68 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: D 179 MET cc_start: 0.8562 (mmm) cc_final: 0.8187 (tpt) REVERT: D 219 MET cc_start: 0.6321 (tmm) cc_final: 0.5991 (tmm) REVERT: E 52 MET cc_start: 0.7488 (tpp) cc_final: 0.7224 (tpt) REVERT: E 56 PHE cc_start: 0.7686 (m-80) cc_final: 0.7231 (m-80) REVERT: E 202 ASP cc_start: 0.7853 (m-30) cc_final: 0.7470 (m-30) REVERT: E 244 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5978 (tt0) REVERT: F 3 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6519 (tt) REVERT: F 20 MET cc_start: 0.2880 (mmt) cc_final: 0.2575 (mmm) REVERT: F 232 ARG cc_start: 0.4583 (OUTLIER) cc_final: 0.2928 (mmp-170) REVERT: G 72 GLU cc_start: 0.7266 (pm20) cc_final: 0.7043 (pm20) REVERT: G 105 MET cc_start: 0.6266 (ttp) cc_final: 0.6018 (ttp) REVERT: G 148 ASP cc_start: 0.7781 (m-30) cc_final: 0.7308 (m-30) REVERT: G 217 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5500 (mp) outliers start: 28 outliers final: 22 residues processed: 155 average time/residue: 0.2214 time to fit residues: 47.8389 Evaluate side-chains 160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 165 MET 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 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 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 F residue 242 LEU 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 192 LEU Chi-restraints excluded: chain G residue 200 ILE 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 24 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** C 243 ASN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.209409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147038 restraints weight = 9008.124| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.57 r_work: 0.3092 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1691 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= 0.165 Angle : 0.467 8.815 12160 Z= 0.244 Chirality : 0.036 0.163 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.314 13.085 1221 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.77 % Allowed : 26.81 % Favored : 70.43 % 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: 3.91 (0.24), residues: 1148 helix: 2.93 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.45 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.001 0.000 HIS E 136 PHE 0.027 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.005 0.000 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4288.73 seconds wall clock time: 75 minutes 23.48 seconds (4523.48 seconds total)