Starting phenix.real_space_refine on Thu Sep 18 16:36:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kch_62251/09_2025/9kch_62251.map" } resolution = 4.19 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 5920 2.51 5 N 1559 2.21 5 O 1605 1.98 5 H 9352 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 18473 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3457 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "B" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3438 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain: "C" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3457 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "D" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3476 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "E" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3457 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "F" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 350 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 391 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "H" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 447 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Time building chain proxies: 2.94, per 1000 atoms: 0.16 Number of scatterers: 18473 At special positions: 0 Unit cell: (85.902, 89.238, 112.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 1605 8.00 N 1559 7.00 C 5920 6.00 H 9352 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 556.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 removed outlier: 3.816A pdb=" N GLU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 77 removed outlier: 6.188A pdb=" N THR A 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 Processing helix chain 'A' and resid 103 through 124 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.573A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.036A pdb=" N THR A 163 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 184 through 222 removed outlier: 4.481A pdb=" N PHE A 222 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 56 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.906A pdb=" N PHE B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 removed outlier: 4.332A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 159 Proline residue: B 138 - end of helix removed outlier: 3.702A pdb=" N ALA B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 220 removed outlier: 4.523A pdb=" N ALA B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Proline residue: B 187 - end of helix removed outlier: 4.308A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 57 removed outlier: 3.947A pdb=" N LYS C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 78 through 95 Processing helix chain 'C' and resid 103 through 124 removed outlier: 3.938A pdb=" N GLY C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 159 removed outlier: 3.864A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.548A pdb=" N TRP C 147 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 224 removed outlier: 4.340A pdb=" N ALA C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 3.648A pdb=" N MET C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 57 removed outlier: 4.111A pdb=" N GLY D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.608A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.570A pdb=" N ALA D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 126 through 157 removed outlier: 3.884A pdb=" N LEU D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.784A pdb=" N ALA D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 184 removed outlier: 3.907A pdb=" N ALA D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 222 removed outlier: 3.536A pdb=" N ALA D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 57 removed outlier: 4.060A pdb=" N ILE E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 4.306A pdb=" N GLY E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 removed outlier: 5.139A pdb=" N THR E 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 96 removed outlier: 3.603A pdb=" N ILE E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 102 No H-bonds generated for 'chain 'E' and resid 100 through 102' Processing helix chain 'E' and resid 103 through 125 removed outlier: 4.397A pdb=" N GLY E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 144 Proline residue: E 138 - end of helix removed outlier: 4.370A pdb=" N GLY E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 removed outlier: 3.598A pdb=" N ALA E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 184 removed outlier: 4.498A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 222 removed outlier: 4.217A pdb=" N ARG E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 222 " --> pdb=" O HIS E 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.991A pdb=" N VAL F 24 " --> pdb=" O PRO F 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 removed outlier: 3.541A pdb=" N VAL G 24 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 33 741 hydrogen bonds defined for protein. 2208 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: 3.77 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9352 1.03 - 1.23: 9 1.23 - 1.42: 3856 1.42 - 1.62: 5357 1.62 - 1.81: 74 Bond restraints: 18648 Sorted by residual: bond pdb=" N SER D 137 " pdb=" CA SER D 137 " ideal model delta sigma weight residual 1.461 1.485 -0.024 9.20e-03 1.18e+04 6.89e+00 bond pdb=" N SER C 28 " pdb=" CA SER C 28 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.15e+00 bond pdb=" C SER C 28 " pdb=" O SER C 28 " ideal model delta sigma weight residual 1.236 1.212 0.025 1.15e-02 7.56e+03 4.65e+00 bond pdb=" N SER D 137 " pdb=" H SER D 137 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.62e+00 bond pdb=" N SER D 31 " pdb=" CA SER D 31 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.59e+00 ... (remaining 18643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 31709 1.44 - 2.89: 1781 2.89 - 4.33: 191 4.33 - 5.78: 41 5.78 - 7.22: 14 Bond angle restraints: 33736 Sorted by residual: angle pdb=" N GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta sigma weight residual 110.28 117.06 -6.78 1.55e+00 4.16e-01 1.91e+01 angle pdb=" N VAL B 167 " pdb=" CA VAL B 167 " pdb=" C VAL B 167 " ideal model delta sigma weight residual 112.12 108.63 3.49 8.40e-01 1.42e+00 1.72e+01 angle pdb=" C GLU A 211 " pdb=" N GLU A 212 " pdb=" CA GLU A 212 " ideal model delta sigma weight residual 120.31 114.09 6.22 1.52e+00 4.33e-01 1.67e+01 angle pdb=" C MET A 210 " pdb=" N GLU A 211 " pdb=" CA GLU A 211 " ideal model delta sigma weight residual 120.31 114.38 5.93 1.52e+00 4.33e-01 1.52e+01 angle pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " pdb=" CG GLU A 211 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 ... (remaining 33731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 7599 16.00 - 32.00: 748 32.00 - 47.99: 161 47.99 - 63.99: 140 63.99 - 79.99: 13 Dihedral angle restraints: 8661 sinusoidal: 4662 harmonic: 3999 Sorted by residual: dihedral pdb=" CA ASN C 75 " pdb=" C ASN C 75 " pdb=" N LEU C 76 " pdb=" CA LEU C 76 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA D 191 " pdb=" C ALA D 191 " pdb=" N TYR D 192 " pdb=" CA TYR D 192 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N PHE C 183 " pdb=" CA PHE C 183 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1094 0.042 - 0.084: 284 0.084 - 0.127: 69 0.127 - 0.169: 6 0.169 - 0.211: 6 Chirality restraints: 1459 Sorted by residual: chirality pdb=" CB THR B 39 " pdb=" CA THR B 39 " pdb=" OG1 THR B 39 " pdb=" CG2 THR B 39 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU A 211 " pdb=" N GLU A 211 " pdb=" C GLU A 211 " pdb=" CB GLU A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR B 132 " pdb=" CA THR B 132 " pdb=" OG1 THR B 132 " pdb=" CG2 THR B 132 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 1456 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 21 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C MET E 21 " 0.055 2.00e-02 2.50e+03 pdb=" O MET E 21 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU E 22 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 208 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ASN C 208 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN C 208 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 209 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 117 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ASN D 117 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN D 117 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 118 " -0.015 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2108 2.25 - 2.84: 41872 2.84 - 3.43: 50319 3.43 - 4.01: 61555 4.01 - 4.60: 96527 Nonbonded interactions: 252381 Sorted by model distance: nonbonded pdb=" OE1 GLU C 106 " pdb=" H GLU C 106 " model vdw 1.665 2.450 nonbonded pdb=" O GLN E 220 " pdb=" H VAL E 224 " model vdw 1.676 2.450 nonbonded pdb=" H GLY C 78 " pdb=" OE2 GLU C 119 " model vdw 1.686 2.450 nonbonded pdb=" OE1 GLU E 80 " pdb=" H GLU E 80 " model vdw 1.687 2.450 nonbonded pdb=" O PHE B 27 " pdb=" HG SER B 31 " model vdw 1.699 2.450 ... (remaining 252376 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' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 9 through 224)) selection = chain 'B' selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 9 through 224)) selection = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 9 through 224)) selection = (chain 'E' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 9 through 224)) } ncs_group { reference = chain 'F' selection = (chain 'G' and ((resid 14 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 15 through \ 34)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.110 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.580 Find NCS groups from input model: 0.200 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9296 Z= 0.198 Angle : 0.794 7.219 12572 Z= 0.450 Chirality : 0.042 0.211 1459 Planarity : 0.005 0.058 1585 Dihedral : 14.030 79.988 3351 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.54 % Favored : 95.28 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % 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: 0.28 (0.24), residues: 1145 helix: 0.77 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 110 TYR 0.012 0.001 TYR E 206 PHE 0.039 0.002 PHE C 183 TRP 0.018 0.001 TRP C 147 HIS 0.010 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9296) covalent geometry : angle 0.79439 (12572) hydrogen bonds : bond 0.10900 ( 741) hydrogen bonds : angle 5.43724 ( 2208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8541 (tp-100) REVERT: A 112 MET cc_start: 0.8049 (mmm) cc_final: 0.7282 (mmm) REVERT: A 121 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 200 ASN cc_start: 0.9363 (m110) cc_final: 0.9113 (m110) REVERT: B 21 MET cc_start: 0.8364 (tmm) cc_final: 0.8160 (tmm) REVERT: B 47 ARG cc_start: 0.9206 (mpt180) cc_final: 0.8811 (mmt-90) REVERT: B 143 PHE cc_start: 0.8754 (m-80) cc_final: 0.8399 (m-10) REVERT: B 211 GLU cc_start: 0.9147 (tp30) cc_final: 0.8721 (tp30) REVERT: C 112 MET cc_start: 0.9223 (mtm) cc_final: 0.8940 (mtm) REVERT: C 124 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 126 HIS cc_start: 0.8353 (m90) cc_final: 0.8142 (m90) REVERT: C 213 PHE cc_start: 0.9309 (t80) cc_final: 0.8878 (t80) REVERT: D 37 GLN cc_start: 0.8646 (mp10) cc_final: 0.8319 (pt0) REVERT: D 50 GLU cc_start: 0.9143 (mp0) cc_final: 0.8931 (pm20) REVERT: D 190 MET cc_start: 0.8826 (mmp) cc_final: 0.8594 (mmm) REVERT: D 200 ASN cc_start: 0.9231 (m-40) cc_final: 0.9000 (m-40) REVERT: D 203 GLU cc_start: 0.9346 (tt0) cc_final: 0.9136 (tt0) REVERT: D 206 TYR cc_start: 0.9325 (m-10) cc_final: 0.8865 (m-10) REVERT: D 210 MET cc_start: 0.9137 (tmm) cc_final: 0.8793 (tmm) REVERT: E 48 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 80 GLU cc_start: 0.8713 (mp0) cc_final: 0.8341 (mp0) REVERT: E 106 GLU cc_start: 0.9138 (mp0) cc_final: 0.8930 (mp0) REVERT: E 151 HIS cc_start: 0.7384 (t70) cc_final: 0.6570 (t70) REVERT: E 207 ASP cc_start: 0.9465 (t0) cc_final: 0.9098 (t0) REVERT: E 210 MET cc_start: 0.9047 (tmm) cc_final: 0.8819 (tmm) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1741 time to fit residues: 82.3353 Evaluate side-chains 296 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN D 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.083763 restraints weight = 92088.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088232 restraints weight = 51431.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091211 restraints weight = 33844.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.093589 restraints weight = 25197.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094987 restraints weight = 19802.326| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9296 Z= 0.142 Angle : 0.541 5.642 12572 Z= 0.309 Chirality : 0.035 0.129 1459 Planarity : 0.004 0.040 1585 Dihedral : 4.293 19.545 1244 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.25), residues: 1145 helix: 1.07 (0.17), residues: 943 sheet: None (None), residues: 0 loop : -2.33 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 110 TYR 0.008 0.001 TYR A 192 PHE 0.026 0.001 PHE C 183 TRP 0.009 0.001 TRP C 147 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9296) covalent geometry : angle 0.54061 (12572) hydrogen bonds : bond 0.04644 ( 741) hydrogen bonds : angle 4.77300 ( 2208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8493 (tp-100) REVERT: A 112 MET cc_start: 0.8063 (mmm) cc_final: 0.7594 (mmm) REVERT: A 200 ASN cc_start: 0.9331 (m110) cc_final: 0.9066 (m110) REVERT: B 47 ARG cc_start: 0.9185 (mpt180) cc_final: 0.8831 (mmt-90) REVERT: B 106 GLU cc_start: 0.9597 (mt-10) cc_final: 0.9304 (mt-10) REVERT: B 117 ASN cc_start: 0.9221 (m-40) cc_final: 0.8922 (m110) REVERT: B 143 PHE cc_start: 0.8597 (m-80) cc_final: 0.8299 (m-10) REVERT: B 211 GLU cc_start: 0.9179 (tp30) cc_final: 0.8756 (tp30) REVERT: C 124 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 126 HIS cc_start: 0.8303 (m90) cc_final: 0.8090 (m90) REVERT: C 211 GLU cc_start: 0.9153 (tt0) cc_final: 0.8484 (tm-30) REVERT: D 106 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8755 (mt-10) REVERT: D 190 MET cc_start: 0.8732 (mmp) cc_final: 0.8411 (mmm) REVERT: D 203 GLU cc_start: 0.9389 (tt0) cc_final: 0.9161 (tt0) REVERT: D 206 TYR cc_start: 0.9286 (m-10) cc_final: 0.8851 (m-10) REVERT: D 210 MET cc_start: 0.9126 (tmm) cc_final: 0.8801 (tmm) REVERT: E 106 GLU cc_start: 0.9085 (mp0) cc_final: 0.8832 (mp0) outliers start: 1 outliers final: 1 residues processed: 324 average time/residue: 0.1663 time to fit residues: 77.3924 Evaluate side-chains 286 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 94 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.111379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.087958 restraints weight = 91784.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.092347 restraints weight = 49938.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.095694 restraints weight = 32626.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.097598 restraints weight = 23221.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.099005 restraints weight = 18626.637| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9296 Z= 0.130 Angle : 0.522 5.923 12572 Z= 0.294 Chirality : 0.035 0.134 1459 Planarity : 0.004 0.054 1585 Dihedral : 4.133 19.319 1244 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.93 (0.25), residues: 1145 helix: 1.25 (0.17), residues: 943 sheet: None (None), residues: 0 loop : -2.36 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 110 TYR 0.006 0.001 TYR E 206 PHE 0.019 0.001 PHE C 183 TRP 0.007 0.001 TRP C 147 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9296) covalent geometry : angle 0.52200 (12572) hydrogen bonds : bond 0.04356 ( 741) hydrogen bonds : angle 4.58633 ( 2208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8545 (tp-100) REVERT: A 105 VAL cc_start: 0.8203 (p) cc_final: 0.7984 (p) REVERT: A 121 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 122 ASN cc_start: 0.8669 (t0) cc_final: 0.8428 (t0) REVERT: B 21 MET cc_start: 0.8178 (tmm) cc_final: 0.7948 (tmm) REVERT: B 117 ASN cc_start: 0.9235 (m-40) cc_final: 0.8930 (m110) REVERT: B 143 PHE cc_start: 0.8639 (m-80) cc_final: 0.8327 (m-10) REVERT: B 150 MET cc_start: 0.9228 (ppp) cc_final: 0.9010 (ppp) REVERT: B 211 GLU cc_start: 0.9167 (tp30) cc_final: 0.8763 (tp30) REVERT: C 121 GLU cc_start: 0.9229 (pm20) cc_final: 0.9027 (mp0) REVERT: C 124 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 126 HIS cc_start: 0.8328 (m90) cc_final: 0.8091 (m90) REVERT: C 189 VAL cc_start: 0.8777 (p) cc_final: 0.8449 (p) REVERT: C 211 GLU cc_start: 0.9182 (tt0) cc_final: 0.8553 (tm-30) REVERT: C 213 PHE cc_start: 0.9292 (t80) cc_final: 0.8870 (t80) REVERT: D 37 GLN cc_start: 0.8698 (mp10) cc_final: 0.8416 (pt0) REVERT: D 106 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8739 (mt-10) REVERT: D 190 MET cc_start: 0.8812 (mmp) cc_final: 0.8404 (mmm) REVERT: D 203 GLU cc_start: 0.9396 (tt0) cc_final: 0.9159 (tt0) REVERT: D 206 TYR cc_start: 0.9274 (m-10) cc_final: 0.8797 (m-10) REVERT: D 212 GLU cc_start: 0.9450 (tt0) cc_final: 0.8650 (tm-30) REVERT: D 216 ILE cc_start: 0.9167 (mm) cc_final: 0.8788 (mm) REVERT: E 211 GLU cc_start: 0.9323 (tm-30) cc_final: 0.9097 (tm-30) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1656 time to fit residues: 76.3225 Evaluate side-chains 281 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.106461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.082317 restraints weight = 93589.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.086675 restraints weight = 52129.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089629 restraints weight = 34205.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.091864 restraints weight = 25388.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.093500 restraints weight = 20328.613| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9296 Z= 0.167 Angle : 0.531 6.187 12572 Z= 0.307 Chirality : 0.035 0.183 1459 Planarity : 0.004 0.035 1585 Dihedral : 4.098 20.819 1244 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.21 % Allowed : 2.12 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.25), residues: 1145 helix: 1.27 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.33 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.008 0.001 TYR A 192 PHE 0.036 0.001 PHE D 27 TRP 0.008 0.001 TRP B 147 HIS 0.002 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9296) covalent geometry : angle 0.53145 (12572) hydrogen bonds : bond 0.04239 ( 741) hydrogen bonds : angle 4.59721 ( 2208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8558 (tp-100) REVERT: A 105 VAL cc_start: 0.8268 (p) cc_final: 0.8057 (p) REVERT: A 121 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8716 (tm-30) REVERT: A 200 ASN cc_start: 0.9343 (m110) cc_final: 0.9074 (m110) REVERT: B 21 MET cc_start: 0.8237 (tmm) cc_final: 0.7981 (tmm) REVERT: B 47 ARG cc_start: 0.9202 (mpt180) cc_final: 0.8851 (mmt-90) REVERT: B 117 ASN cc_start: 0.9214 (m-40) cc_final: 0.8907 (m110) REVERT: B 143 PHE cc_start: 0.8611 (m-80) cc_final: 0.8329 (m-10) REVERT: B 150 MET cc_start: 0.9249 (ppp) cc_final: 0.9038 (ppp) REVERT: B 211 GLU cc_start: 0.9212 (tp30) cc_final: 0.8772 (tp30) REVERT: C 121 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.9016 (pp20) REVERT: C 124 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8801 (tm-30) REVERT: C 126 HIS cc_start: 0.8342 (m90) cc_final: 0.8117 (m90) REVERT: C 211 GLU cc_start: 0.9219 (tt0) cc_final: 0.8602 (tm-30) REVERT: C 213 PHE cc_start: 0.9338 (t80) cc_final: 0.8930 (t80) REVERT: D 37 GLN cc_start: 0.8607 (mp10) cc_final: 0.8360 (pt0) REVERT: D 106 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8744 (mt-10) REVERT: D 190 MET cc_start: 0.8809 (mmp) cc_final: 0.8387 (mmm) REVERT: D 203 GLU cc_start: 0.9409 (tt0) cc_final: 0.9197 (tt0) REVERT: D 206 TYR cc_start: 0.9278 (m-10) cc_final: 0.8792 (m-10) REVERT: D 212 GLU cc_start: 0.9487 (tt0) cc_final: 0.8709 (tm-30) REVERT: D 216 ILE cc_start: 0.9151 (mm) cc_final: 0.8757 (mm) REVERT: E 211 GLU cc_start: 0.9310 (tm-30) cc_final: 0.9089 (tm-30) outliers start: 2 outliers final: 0 residues processed: 314 average time/residue: 0.1660 time to fit residues: 75.3531 Evaluate side-chains 282 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN D 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.109935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.086867 restraints weight = 91262.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.091336 restraints weight = 48999.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.094441 restraints weight = 31237.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096812 restraints weight = 22569.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098106 restraints weight = 17512.677| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9296 Z= 0.147 Angle : 0.529 6.151 12572 Z= 0.304 Chirality : 0.035 0.131 1459 Planarity : 0.003 0.034 1585 Dihedral : 4.061 20.409 1244 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 1.05 (0.25), residues: 1145 helix: 1.33 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -2.30 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.014 0.001 TYR C 192 PHE 0.045 0.002 PHE E 213 TRP 0.007 0.001 TRP B 147 HIS 0.003 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9296) covalent geometry : angle 0.52933 (12572) hydrogen bonds : bond 0.04225 ( 741) hydrogen bonds : angle 4.58827 ( 2208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8561 (tp-100) REVERT: A 105 VAL cc_start: 0.8253 (p) cc_final: 0.8044 (p) REVERT: A 121 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8705 (tm-30) REVERT: B 117 ASN cc_start: 0.9223 (m-40) cc_final: 0.8923 (m110) REVERT: B 150 MET cc_start: 0.9247 (ppp) cc_final: 0.9029 (ppp) REVERT: B 211 GLU cc_start: 0.9190 (tp30) cc_final: 0.8722 (tp30) REVERT: C 121 GLU cc_start: 0.9270 (pm20) cc_final: 0.9062 (mp0) REVERT: C 124 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8808 (tm-30) REVERT: C 126 HIS cc_start: 0.8383 (m90) cc_final: 0.8151 (m90) REVERT: C 211 GLU cc_start: 0.9200 (tt0) cc_final: 0.8566 (tm-30) REVERT: C 213 PHE cc_start: 0.9304 (t80) cc_final: 0.8889 (t80) REVERT: D 37 GLN cc_start: 0.8600 (mp10) cc_final: 0.8364 (pt0) REVERT: D 106 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8714 (mt-10) REVERT: D 190 MET cc_start: 0.8819 (mmp) cc_final: 0.8391 (mmm) REVERT: D 203 GLU cc_start: 0.9382 (tt0) cc_final: 0.9156 (tt0) REVERT: D 206 TYR cc_start: 0.9281 (m-10) cc_final: 0.8783 (m-10) REVERT: D 212 GLU cc_start: 0.9485 (tt0) cc_final: 0.8728 (tm-30) REVERT: D 216 ILE cc_start: 0.9142 (mm) cc_final: 0.8772 (mm) REVERT: E 211 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9125 (tm-30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1589 time to fit residues: 73.0332 Evaluate side-chains 281 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.108843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.085119 restraints weight = 92462.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.089590 restraints weight = 48938.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.092399 restraints weight = 31140.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.094646 restraints weight = 23005.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.096563 restraints weight = 18045.944| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9296 Z= 0.189 Angle : 0.552 6.274 12572 Z= 0.321 Chirality : 0.035 0.131 1459 Planarity : 0.004 0.036 1585 Dihedral : 4.115 20.414 1244 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.25), residues: 1145 helix: 1.28 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.010 0.001 TYR A 192 PHE 0.044 0.002 PHE E 213 TRP 0.008 0.001 TRP B 147 HIS 0.003 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9296) covalent geometry : angle 0.55196 (12572) hydrogen bonds : bond 0.04183 ( 741) hydrogen bonds : angle 4.67713 ( 2208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8598 (tp-100) REVERT: A 121 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8791 (tm-30) REVERT: A 200 ASN cc_start: 0.9328 (m110) cc_final: 0.9083 (m110) REVERT: B 21 MET cc_start: 0.8217 (tmm) cc_final: 0.8013 (tmm) REVERT: B 117 ASN cc_start: 0.9228 (m-40) cc_final: 0.8930 (m110) REVERT: B 150 MET cc_start: 0.9262 (ppp) cc_final: 0.9047 (ppp) REVERT: B 211 GLU cc_start: 0.9246 (tp30) cc_final: 0.8839 (tp30) REVERT: C 124 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8897 (tm-30) REVERT: C 126 HIS cc_start: 0.8327 (m90) cc_final: 0.8123 (m90) REVERT: C 211 GLU cc_start: 0.9228 (tt0) cc_final: 0.8622 (tm-30) REVERT: D 37 GLN cc_start: 0.8610 (mp10) cc_final: 0.8386 (pt0) REVERT: D 190 MET cc_start: 0.8684 (mmp) cc_final: 0.8280 (mmp) REVERT: D 203 GLU cc_start: 0.9406 (tt0) cc_final: 0.9205 (tt0) REVERT: D 206 TYR cc_start: 0.9301 (m-10) cc_final: 0.8821 (m-10) REVERT: D 212 GLU cc_start: 0.9501 (tt0) cc_final: 0.8894 (tm-30) REVERT: D 216 ILE cc_start: 0.9189 (mm) cc_final: 0.8904 (mm) REVERT: E 21 MET cc_start: 0.8129 (ttp) cc_final: 0.7900 (tmm) REVERT: E 121 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8343 (tm-30) REVERT: E 122 ASN cc_start: 0.8845 (p0) cc_final: 0.8565 (p0) REVERT: E 211 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9138 (tm-30) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1630 time to fit residues: 72.5140 Evaluate side-chains 279 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.109969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086017 restraints weight = 91774.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.090503 restraints weight = 47961.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.093790 restraints weight = 30686.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096200 restraints weight = 22031.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.097560 restraints weight = 16895.976| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9296 Z= 0.150 Angle : 0.531 6.176 12572 Z= 0.302 Chirality : 0.035 0.135 1459 Planarity : 0.003 0.035 1585 Dihedral : 4.091 20.354 1244 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 1.09 (0.25), residues: 1145 helix: 1.37 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -2.33 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.011 0.001 TYR E 206 PHE 0.035 0.002 PHE E 213 TRP 0.008 0.001 TRP B 147 HIS 0.003 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9296) covalent geometry : angle 0.53054 (12572) hydrogen bonds : bond 0.04049 ( 741) hydrogen bonds : angle 4.57633 ( 2208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8605 (tp-100) REVERT: A 121 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 200 ASN cc_start: 0.9307 (m110) cc_final: 0.9044 (m110) REVERT: B 21 MET cc_start: 0.8165 (tmm) cc_final: 0.7961 (tmm) REVERT: B 47 ARG cc_start: 0.9226 (mpt180) cc_final: 0.8861 (mmt-90) REVERT: B 117 ASN cc_start: 0.9221 (m-40) cc_final: 0.8924 (m110) REVERT: B 150 MET cc_start: 0.9258 (ppp) cc_final: 0.9041 (ppp) REVERT: B 211 GLU cc_start: 0.9235 (tp30) cc_final: 0.8825 (tp30) REVERT: C 124 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8823 (tm-30) REVERT: C 126 HIS cc_start: 0.8314 (m90) cc_final: 0.8103 (m90) REVERT: C 211 GLU cc_start: 0.9201 (tt0) cc_final: 0.8628 (tm-30) REVERT: D 37 GLN cc_start: 0.8600 (mp10) cc_final: 0.8376 (pt0) REVERT: D 106 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8730 (mt-10) REVERT: D 190 MET cc_start: 0.8644 (mmp) cc_final: 0.8253 (mmp) REVERT: D 203 GLU cc_start: 0.9394 (tt0) cc_final: 0.9157 (tt0) REVERT: D 212 GLU cc_start: 0.9494 (tt0) cc_final: 0.8886 (tm-30) REVERT: D 213 PHE cc_start: 0.9196 (t80) cc_final: 0.8957 (t80) REVERT: D 216 ILE cc_start: 0.9193 (mm) cc_final: 0.8905 (mm) REVERT: E 121 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8356 (tm-30) REVERT: E 122 ASN cc_start: 0.8828 (p0) cc_final: 0.8547 (p0) REVERT: E 211 GLU cc_start: 0.9356 (tm-30) cc_final: 0.9151 (tm-30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1630 time to fit residues: 72.7916 Evaluate side-chains 284 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 208 ASN E 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.106876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081947 restraints weight = 92491.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.086391 restraints weight = 50231.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.089317 restraints weight = 32655.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.091654 restraints weight = 24277.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.093105 restraints weight = 19204.926| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9296 Z= 0.179 Angle : 0.543 6.292 12572 Z= 0.315 Chirality : 0.036 0.143 1459 Planarity : 0.004 0.036 1585 Dihedral : 4.110 20.156 1244 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.94 (0.25), residues: 1145 helix: 1.25 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.010 0.001 TYR A 192 PHE 0.042 0.002 PHE E 213 TRP 0.008 0.001 TRP B 147 HIS 0.004 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9296) covalent geometry : angle 0.54262 (12572) hydrogen bonds : bond 0.04128 ( 741) hydrogen bonds : angle 4.67502 ( 2208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8619 (tp-100) REVERT: A 112 MET cc_start: 0.8164 (mmm) cc_final: 0.7762 (mmm) REVERT: A 121 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 200 ASN cc_start: 0.9287 (m110) cc_final: 0.9020 (m110) REVERT: B 21 MET cc_start: 0.8206 (tmm) cc_final: 0.7987 (tmm) REVERT: B 117 ASN cc_start: 0.9200 (m-40) cc_final: 0.8909 (m110) REVERT: B 150 MET cc_start: 0.9274 (ppp) cc_final: 0.9064 (ppp) REVERT: B 211 GLU cc_start: 0.9250 (tp30) cc_final: 0.8839 (tp30) REVERT: C 124 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 126 HIS cc_start: 0.8327 (m90) cc_final: 0.8125 (m90) REVERT: C 211 GLU cc_start: 0.9200 (tt0) cc_final: 0.8631 (tm-30) REVERT: D 37 GLN cc_start: 0.8541 (mp10) cc_final: 0.8319 (pt0) REVERT: D 106 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8753 (mt-10) REVERT: D 190 MET cc_start: 0.8586 (mmp) cc_final: 0.8220 (mmp) REVERT: D 200 ASN cc_start: 0.9300 (m-40) cc_final: 0.9054 (m110) REVERT: D 203 GLU cc_start: 0.9393 (tt0) cc_final: 0.9160 (tt0) REVERT: D 212 GLU cc_start: 0.9496 (tt0) cc_final: 0.8922 (tm-30) REVERT: D 213 PHE cc_start: 0.9218 (t80) cc_final: 0.8984 (t80) REVERT: D 216 ILE cc_start: 0.9223 (mm) cc_final: 0.8944 (mm) REVERT: E 121 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8305 (tm-30) REVERT: E 122 ASN cc_start: 0.8782 (p0) cc_final: 0.8500 (p0) REVERT: E 211 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9147 (tm-30) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1595 time to fit residues: 72.1940 Evaluate side-chains 285 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.109183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085450 restraints weight = 91930.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090045 restraints weight = 47946.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.093062 restraints weight = 30290.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.095502 restraints weight = 22034.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097047 restraints weight = 17051.277| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9296 Z= 0.169 Angle : 0.539 6.259 12572 Z= 0.310 Chirality : 0.036 0.135 1459 Planarity : 0.004 0.037 1585 Dihedral : 4.135 19.963 1244 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.95 (0.25), residues: 1145 helix: 1.26 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.36 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.014 0.001 TYR E 206 PHE 0.043 0.002 PHE E 213 TRP 0.008 0.001 TRP B 147 HIS 0.004 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9296) covalent geometry : angle 0.53876 (12572) hydrogen bonds : bond 0.04035 ( 741) hydrogen bonds : angle 4.62528 ( 2208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8658 (tp-100) REVERT: B 47 ARG cc_start: 0.9225 (mpt180) cc_final: 0.8823 (mmt-90) REVERT: B 117 ASN cc_start: 0.9219 (m-40) cc_final: 0.8925 (m110) REVERT: B 150 MET cc_start: 0.9283 (ppp) cc_final: 0.9062 (ppp) REVERT: B 211 GLU cc_start: 0.9253 (tp30) cc_final: 0.8851 (tp30) REVERT: C 124 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 126 HIS cc_start: 0.8352 (m90) cc_final: 0.8150 (m90) REVERT: C 211 GLU cc_start: 0.9216 (tt0) cc_final: 0.8639 (tm-30) REVERT: C 213 PHE cc_start: 0.9417 (t80) cc_final: 0.8871 (t80) REVERT: D 106 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8720 (mt-10) REVERT: D 190 MET cc_start: 0.8624 (mmp) cc_final: 0.8244 (mmp) REVERT: D 200 ASN cc_start: 0.9314 (m-40) cc_final: 0.9061 (m110) REVERT: D 203 GLU cc_start: 0.9408 (tt0) cc_final: 0.9180 (tt0) REVERT: D 212 GLU cc_start: 0.9487 (tt0) cc_final: 0.8923 (tm-30) REVERT: D 213 PHE cc_start: 0.9202 (t80) cc_final: 0.8974 (t80) REVERT: D 216 ILE cc_start: 0.9211 (mm) cc_final: 0.8907 (mm) REVERT: E 121 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8419 (tm-30) REVERT: E 122 ASN cc_start: 0.8823 (p0) cc_final: 0.8557 (p0) REVERT: E 211 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9196 (tm-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1628 time to fit residues: 73.3928 Evaluate side-chains 286 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.110776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.086746 restraints weight = 90049.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.091497 restraints weight = 46735.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.094609 restraints weight = 29348.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.097184 restraints weight = 21203.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.098538 restraints weight = 16145.696| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9296 Z= 0.120 Angle : 0.534 6.345 12572 Z= 0.296 Chirality : 0.035 0.139 1459 Planarity : 0.003 0.029 1585 Dihedral : 4.036 19.369 1244 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.25 (0.25), residues: 1145 helix: 1.48 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.30 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 73 TYR 0.013 0.001 TYR C 84 PHE 0.047 0.002 PHE E 213 TRP 0.007 0.001 TRP E 57 HIS 0.004 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9296) covalent geometry : angle 0.53420 (12572) hydrogen bonds : bond 0.03921 ( 741) hydrogen bonds : angle 4.34731 ( 2208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8633 (tp-100) REVERT: A 200 ASN cc_start: 0.9260 (m110) cc_final: 0.9001 (m110) REVERT: A 207 ASP cc_start: 0.9314 (m-30) cc_final: 0.9098 (m-30) REVERT: B 21 MET cc_start: 0.8384 (tmm) cc_final: 0.8178 (tmm) REVERT: B 117 ASN cc_start: 0.9213 (m-40) cc_final: 0.8924 (m110) REVERT: B 150 MET cc_start: 0.9262 (ppp) cc_final: 0.9048 (ppp) REVERT: B 211 GLU cc_start: 0.9238 (tp30) cc_final: 0.8811 (tp30) REVERT: C 124 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 126 HIS cc_start: 0.8334 (m90) cc_final: 0.8087 (m90) REVERT: C 211 GLU cc_start: 0.9177 (tt0) cc_final: 0.8605 (tm-30) REVERT: C 213 PHE cc_start: 0.9422 (t80) cc_final: 0.8852 (t80) REVERT: D 106 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8746 (mt-10) REVERT: D 190 MET cc_start: 0.8630 (mmp) cc_final: 0.8236 (mmp) REVERT: D 200 ASN cc_start: 0.9303 (m-40) cc_final: 0.9050 (m110) REVERT: D 203 GLU cc_start: 0.9391 (tt0) cc_final: 0.9163 (tt0) REVERT: D 212 GLU cc_start: 0.9512 (tt0) cc_final: 0.8893 (tm-30) REVERT: D 213 PHE cc_start: 0.9195 (t80) cc_final: 0.8932 (t80) REVERT: D 216 ILE cc_start: 0.9217 (mm) cc_final: 0.8911 (mm) REVERT: E 106 GLU cc_start: 0.9173 (mp0) cc_final: 0.8887 (mp0) REVERT: E 121 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8398 (tm-30) REVERT: E 122 ASN cc_start: 0.8861 (p0) cc_final: 0.8585 (p0) REVERT: E 211 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9174 (tm-30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1720 time to fit residues: 78.5520 Evaluate side-chains 285 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.109368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086594 restraints weight = 92724.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090800 restraints weight = 49759.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.093983 restraints weight = 32289.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096310 restraints weight = 23577.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.097528 restraints weight = 18158.477| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9296 Z= 0.135 Angle : 0.537 6.355 12572 Z= 0.304 Chirality : 0.035 0.146 1459 Planarity : 0.003 0.028 1585 Dihedral : 4.010 19.240 1244 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.22 (0.25), residues: 1145 helix: 1.46 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.006 0.001 TYR A 192 PHE 0.026 0.001 PHE D 27 TRP 0.007 0.001 TRP D 147 HIS 0.004 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9296) covalent geometry : angle 0.53674 (12572) hydrogen bonds : bond 0.03941 ( 741) hydrogen bonds : angle 4.45494 ( 2208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.41 seconds wall clock time: 49 minutes 36.99 seconds (2976.99 seconds total)