Starting phenix.real_space_refine on Wed Feb 4 07:02:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw1_47233/02_2026/9dw1_47233.map" } resolution = 3.4 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 5796 2.51 5 N 1551 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9090 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1268 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain breaks: 1 Chain: "I" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1270 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1249 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Chain: "M" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1249 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Chain: "N" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1352 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain breaks: 2 Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 9090 At special positions: 0 Unit cell: (116.56, 114.68, 63.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 1652 8.00 N 1551 7.00 C 5796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 286.9 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 17 sheets defined 52.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 74 through 81 Processing helix chain 'H' and resid 92 through 110 removed outlier: 3.645A pdb=" N SER H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 139 removed outlier: 3.660A pdb=" N ALA H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 161 removed outlier: 3.942A pdb=" N LEU H 158 " --> pdb=" O MET H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.509A pdb=" N ASN H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 231 through 239 removed outlier: 3.788A pdb=" N GLU H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 81 removed outlier: 3.619A pdb=" N ARG I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 110 removed outlier: 3.647A pdb=" N LEU I 98 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 104 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 139 removed outlier: 3.913A pdb=" N ALA I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 161 removed outlier: 3.600A pdb=" N LEU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU I 159 " --> pdb=" O GLY I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 214 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 231 through 239 removed outlier: 3.554A pdb=" N GLU I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 79 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 92 through 110 removed outlier: 3.653A pdb=" N SER J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 139 removed outlier: 3.611A pdb=" N ALA J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR J 135 " --> pdb=" O ALA J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 162 removed outlier: 3.884A pdb=" N LEU J 157 " --> pdb=" O SER J 153 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 159 " --> pdb=" O GLY J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 214 Processing helix chain 'J' and resid 216 through 224 Processing helix chain 'J' and resid 231 through 239 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.503A pdb=" N TYR K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG K 81 " --> pdb=" O SER K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 110 removed outlier: 4.302A pdb=" N LEU K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 139 removed outlier: 4.056A pdb=" N ALA K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 161 Processing helix chain 'K' and resid 196 through 214 Processing helix chain 'K' and resid 216 through 225 Processing helix chain 'K' and resid 231 through 239 removed outlier: 3.656A pdb=" N GLU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'L' and resid 92 through 110 removed outlier: 3.596A pdb=" N LEU L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 108 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 139 removed outlier: 4.317A pdb=" N ALA L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 162 removed outlier: 3.537A pdb=" N GLY L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.080A pdb=" N GLN L 204 " --> pdb=" O LYS L 200 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU L 205 " --> pdb=" O LEU L 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN L 207 " --> pdb=" O LYS L 203 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS L 212 " --> pdb=" O ILE L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 224 removed outlier: 3.620A pdb=" N SER L 222 " --> pdb=" O GLN L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 239 removed outlier: 3.828A pdb=" N GLU L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 81 removed outlier: 3.565A pdb=" N LEU M 80 " --> pdb=" O TYR M 76 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG M 81 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 110 removed outlier: 3.584A pdb=" N SER M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 139 removed outlier: 4.269A pdb=" N ALA M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 161 removed outlier: 3.552A pdb=" N LEU M 157 " --> pdb=" O SER M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 214 Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 231 through 239 removed outlier: 4.008A pdb=" N GLU M 237 " --> pdb=" O MET M 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 80 Processing helix chain 'N' and resid 92 through 110 removed outlier: 4.024A pdb=" N LEU N 98 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 139 removed outlier: 3.898A pdb=" N ALA N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 161 Processing helix chain 'N' and resid 196 through 213 removed outlier: 3.864A pdb=" N GLN N 204 " --> pdb=" O LYS N 200 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU N 205 " --> pdb=" O LEU N 201 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN N 207 " --> pdb=" O LYS N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 224 Processing helix chain 'N' and resid 231 through 239 removed outlier: 3.718A pdb=" N GLU N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.740A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.740A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS H 243 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 84 through 88 removed outlier: 5.855A pdb=" N SER I 121 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN I 150 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG I 174 " --> pdb=" O CYS I 147 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY I 149 " --> pdb=" O ARG I 174 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET I 176 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA I 151 " --> pdb=" O MET I 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 84 through 88 removed outlier: 5.855A pdb=" N SER I 121 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN I 150 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS I 168 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR I 145 " --> pdb=" O HIS I 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 61 through 64 Processing sheet with id=AA6, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.573A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.573A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS J 168 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR J 145 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG J 167 " --> pdb=" O LYS J 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 88 removed outlier: 5.542A pdb=" N SER K 121 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN K 150 " --> pdb=" O SER K 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 84 through 88 removed outlier: 5.542A pdb=" N SER K 121 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN K 150 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS K 168 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR K 145 " --> pdb=" O HIS K 168 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG K 167 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 84 through 88 removed outlier: 5.486A pdb=" N SER L 121 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN L 150 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 84 through 88 removed outlier: 5.486A pdb=" N SER L 121 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN L 150 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS L 168 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR L 145 " --> pdb=" O HIS L 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 84 through 88 removed outlier: 5.721A pdb=" N SER M 121 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN M 150 " --> pdb=" O SER M 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 84 through 88 removed outlier: 5.721A pdb=" N SER M 121 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN M 150 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS M 168 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR M 145 " --> pdb=" O HIS M 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 61 through 63 Processing sheet with id=AB6, first strand: chain 'N' and resid 84 through 88 Processing sheet with id=AB7, first strand: chain 'N' and resid 150 through 152 Processing sheet with id=AB8, first strand: chain 'N' and resid 168 through 169 508 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2480 1.33 - 1.45: 1293 1.45 - 1.57: 5318 1.57 - 1.69: 0 1.69 - 1.81: 161 Bond restraints: 9252 Sorted by residual: bond pdb=" CG1 ILE I 139 " pdb=" CD1 ILE I 139 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CA ILE I 59 " pdb=" CB ILE I 59 " ideal model delta sigma weight residual 1.537 1.551 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" CG1 ILE K 139 " pdb=" CD1 ILE K 139 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" C PRO J 248 " pdb=" N PRO J 249 " ideal model delta sigma weight residual 1.341 1.357 -0.016 1.60e-02 3.91e+03 1.03e+00 bond pdb=" N SER M 153 " pdb=" CA SER M 153 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.45e-01 ... (remaining 9247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12176 1.65 - 3.30: 293 3.30 - 4.95: 26 4.95 - 6.61: 1 6.61 - 8.26: 3 Bond angle restraints: 12499 Sorted by residual: angle pdb=" N PRO L 114 " pdb=" CA PRO L 114 " pdb=" C PRO L 114 " ideal model delta sigma weight residual 111.34 115.31 -3.97 1.55e+00 4.16e-01 6.54e+00 angle pdb=" C SER M 153 " pdb=" CA SER M 153 " pdb=" CB SER M 153 " ideal model delta sigma weight residual 110.42 115.46 -5.04 1.99e+00 2.53e-01 6.41e+00 angle pdb=" N PRO K 114 " pdb=" CA PRO K 114 " pdb=" C PRO K 114 " ideal model delta sigma weight residual 111.34 114.83 -3.49 1.55e+00 4.16e-01 5.06e+00 angle pdb=" N PRO L 164 " pdb=" CA PRO L 164 " pdb=" C PRO L 164 " ideal model delta sigma weight residual 111.26 114.93 -3.67 1.63e+00 3.76e-01 5.06e+00 angle pdb=" CA GLU M 82 " pdb=" CB GLU M 82 " pdb=" CG GLU M 82 " ideal model delta sigma weight residual 114.10 118.50 -4.40 2.00e+00 2.50e-01 4.84e+00 ... (remaining 12494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5327 17.92 - 35.84: 299 35.84 - 53.75: 58 53.75 - 71.67: 18 71.67 - 89.59: 15 Dihedral angle restraints: 5717 sinusoidal: 2318 harmonic: 3399 Sorted by residual: dihedral pdb=" CA GLN I 150 " pdb=" C GLN I 150 " pdb=" N ALA I 151 " pdb=" CA ALA I 151 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA THR N 145 " pdb=" C THR N 145 " pdb=" N TRP N 146 " pdb=" CA TRP N 146 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLU N 109 " pdb=" C GLU N 109 " pdb=" N SER N 110 " pdb=" CA SER N 110 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 910 0.037 - 0.073: 375 0.073 - 0.110: 112 0.110 - 0.146: 41 0.146 - 0.183: 5 Chirality restraints: 1443 Sorted by residual: chirality pdb=" CA ILE I 59 " pdb=" N ILE I 59 " pdb=" C ILE I 59 " pdb=" CB ILE I 59 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA ILE H 115 " pdb=" N ILE H 115 " pdb=" C ILE H 115 " pdb=" CB ILE H 115 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE H 119 " pdb=" N ILE H 119 " pdb=" C ILE H 119 " pdb=" CB ILE H 119 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1440 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 83 " 0.213 9.50e-02 1.11e+02 9.60e-02 7.20e+00 pdb=" NE ARG J 83 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG J 83 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG J 83 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 83 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 228 " -0.187 9.50e-02 1.11e+02 8.43e-02 5.56e+00 pdb=" NE ARG J 228 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG J 228 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG J 228 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 228 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 174 " 0.157 9.50e-02 1.11e+02 7.10e-02 3.88e+00 pdb=" NE ARG J 174 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 174 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG J 174 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG J 174 " 0.001 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2605 2.84 - 3.36: 8773 3.36 - 3.87: 14225 3.87 - 4.39: 17496 4.39 - 4.90: 29464 Nonbonded interactions: 72563 Sorted by model distance: nonbonded pdb=" OG1 THR J 66 " pdb=" O GLY J 69 " model vdw 2.326 3.040 nonbonded pdb=" OG SER I 77 " pdb=" O ILE J 61 " model vdw 2.341 3.040 nonbonded pdb=" O ASN M 111 " pdb=" ND2 ASN M 111 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN I 172 " pdb=" OD1 ASP N 134 " model vdw 2.382 3.120 nonbonded pdb=" OE2 GLU N 64 " pdb=" NH1 ARG N 78 " model vdw 2.388 3.120 ... (remaining 72558 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 'H' and resid 74 through 247) selection = (chain 'I' and resid 74 through 247) selection = (chain 'J' and resid 74 through 247) selection = (chain 'K' and resid 74 through 247) selection = (chain 'L' and resid 74 through 247) selection = (chain 'M' and resid 74 through 247) selection = (chain 'N' and resid 74 through 247) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9252 Z= 0.141 Angle : 0.631 8.256 12499 Z= 0.364 Chirality : 0.046 0.183 1443 Planarity : 0.007 0.096 1574 Dihedral : 13.328 89.591 3519 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.69 % Allowed : 2.38 % Favored : 96.93 % 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 are not related in a simple way. whole: -2.63 (0.20), residues: 1130 helix: -2.34 (0.16), residues: 593 sheet: -1.01 (0.39), residues: 132 loop : -0.62 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG J 83 TYR 0.019 0.004 TYR M 138 PHE 0.008 0.001 PHE N 238 TRP 0.018 0.002 TRP M 146 HIS 0.005 0.001 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9252) covalent geometry : angle 0.63069 (12499) hydrogen bonds : bond 0.23271 ( 454) hydrogen bonds : angle 8.50185 ( 1497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 210 time to evaluate : 0.311 Fit side-chains REVERT: H 81 ARG cc_start: 0.7894 (ptm-80) cc_final: 0.7485 (mtp-110) REVERT: H 112 LYS cc_start: 0.8440 (mttt) cc_final: 0.8229 (mmtm) REVERT: H 199 MET cc_start: 0.7586 (tmm) cc_final: 0.7172 (tpt) REVERT: H 211 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8748 (ttpp) REVERT: I 81 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8128 (mtm110) REVERT: I 173 SER cc_start: 0.8430 (m) cc_final: 0.8176 (p) REVERT: I 176 MET cc_start: 0.8208 (ttp) cc_final: 0.8002 (ttp) REVERT: I 199 MET cc_start: 0.7784 (tpt) cc_final: 0.7572 (tmm) REVERT: K 110 SER cc_start: 0.8709 (t) cc_final: 0.8393 (m) REVERT: K 199 MET cc_start: 0.7298 (tmm) cc_final: 0.7048 (tmm) REVERT: L 111 ASN cc_start: 0.8708 (t0) cc_final: 0.8387 (t0) REVERT: L 203 LYS cc_start: 0.8571 (tppp) cc_final: 0.8038 (tptp) REVERT: M 137 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8384 (mm110) REVERT: M 199 MET cc_start: 0.7185 (tpt) cc_final: 0.6742 (tpp) REVERT: N 97 SER cc_start: 0.8887 (t) cc_final: 0.8592 (m) REVERT: N 200 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8062 (ttpp) outliers start: 7 outliers final: 3 residues processed: 215 average time/residue: 0.1039 time to fit residues: 29.1279 Evaluate side-chains 181 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain M residue 80 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 215 GLN K 204 GLN L 102 GLN L 141 ASN M 102 GLN M 141 ASN N 111 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103896 restraints weight = 10775.644| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.02 r_work: 0.2948 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9252 Z= 0.147 Angle : 0.600 8.071 12499 Z= 0.317 Chirality : 0.045 0.183 1443 Planarity : 0.005 0.033 1574 Dihedral : 5.634 57.928 1257 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.99 % Allowed : 8.13 % Favored : 90.88 % 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 are not related in a simple way. whole: -0.89 (0.23), residues: 1130 helix: -0.64 (0.19), residues: 608 sheet: -0.41 (0.40), residues: 130 loop : -0.22 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 226 TYR 0.016 0.001 TYR M 138 PHE 0.012 0.002 PHE K 105 TRP 0.013 0.002 TRP M 146 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9252) covalent geometry : angle 0.59979 (12499) hydrogen bonds : bond 0.04883 ( 454) hydrogen bonds : angle 4.87972 ( 1497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.248 Fit side-chains REVERT: H 81 ARG cc_start: 0.7791 (ptm-80) cc_final: 0.7329 (mtp-110) REVERT: H 166 MET cc_start: 0.7999 (mtt) cc_final: 0.7554 (mtp) REVERT: H 199 MET cc_start: 0.7396 (tmm) cc_final: 0.6896 (tpt) REVERT: I 166 MET cc_start: 0.8546 (mtt) cc_final: 0.8281 (mtp) REVERT: I 173 SER cc_start: 0.8390 (m) cc_final: 0.8125 (p) REVERT: I 199 MET cc_start: 0.7579 (tpt) cc_final: 0.7319 (tmm) REVERT: K 110 SER cc_start: 0.8429 (t) cc_final: 0.8131 (m) REVERT: K 199 MET cc_start: 0.7075 (tmm) cc_final: 0.6715 (tmm) REVERT: K 228 ARG cc_start: 0.8255 (ptt90) cc_final: 0.7947 (ptt-90) REVERT: K 234 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7112 (tt0) REVERT: L 78 ARG cc_start: 0.8259 (tpt90) cc_final: 0.7360 (tpt90) REVERT: L 81 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7571 (ttp-110) REVERT: L 111 ASN cc_start: 0.8784 (t0) cc_final: 0.8513 (t0) REVERT: L 203 LYS cc_start: 0.8106 (tppp) cc_final: 0.7689 (mmmt) REVERT: L 233 MET cc_start: 0.8052 (tpp) cc_final: 0.7817 (tpt) REVERT: M 80 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7018 (tt) REVERT: M 199 MET cc_start: 0.7121 (tpt) cc_final: 0.6710 (tpp) REVERT: N 97 SER cc_start: 0.9125 (t) cc_final: 0.8796 (m) REVERT: N 178 HIS cc_start: 0.8657 (t-90) cc_final: 0.8397 (t-90) REVERT: N 199 MET cc_start: 0.7629 (tmm) cc_final: 0.7175 (tmm) outliers start: 10 outliers final: 6 residues processed: 197 average time/residue: 0.1087 time to fit residues: 27.3595 Evaluate side-chains 185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 214 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 141 ASN I 247 HIS J 172 ASN J 215 GLN M 111 ASN N 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101183 restraints weight = 10789.645| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.31 r_work: 0.2903 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9252 Z= 0.136 Angle : 0.551 8.413 12499 Z= 0.282 Chirality : 0.044 0.157 1443 Planarity : 0.004 0.041 1574 Dihedral : 4.919 49.286 1256 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 9.71 % Favored : 88.60 % 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 are not related in a simple way. whole: -0.31 (0.24), residues: 1130 helix: -0.00 (0.20), residues: 608 sheet: -0.37 (0.40), residues: 130 loop : -0.18 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 83 TYR 0.015 0.001 TYR M 138 PHE 0.015 0.002 PHE L 105 TRP 0.010 0.002 TRP M 146 HIS 0.003 0.001 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9252) covalent geometry : angle 0.55111 (12499) hydrogen bonds : bond 0.03796 ( 454) hydrogen bonds : angle 4.30624 ( 1497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.342 Fit side-chains REVERT: H 81 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7259 (mtp-110) REVERT: H 166 MET cc_start: 0.8062 (mtt) cc_final: 0.7787 (mtp) REVERT: H 199 MET cc_start: 0.7181 (tmm) cc_final: 0.6676 (tpt) REVERT: H 233 MET cc_start: 0.8387 (tpp) cc_final: 0.8181 (tpp) REVERT: I 166 MET cc_start: 0.8409 (mtt) cc_final: 0.8143 (mtp) REVERT: I 173 SER cc_start: 0.8416 (m) cc_final: 0.8144 (p) REVERT: I 228 ARG cc_start: 0.7648 (ptm160) cc_final: 0.7286 (ptm-80) REVERT: J 215 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8112 (mm-40) REVERT: K 110 SER cc_start: 0.8434 (t) cc_final: 0.8120 (m) REVERT: K 154 MET cc_start: 0.7879 (mmm) cc_final: 0.7526 (mmm) REVERT: K 166 MET cc_start: 0.7952 (mtp) cc_final: 0.7596 (mtp) REVERT: K 199 MET cc_start: 0.7158 (tmm) cc_final: 0.6658 (tmm) REVERT: K 226 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7659 (mtm180) REVERT: K 228 ARG cc_start: 0.8193 (ptt90) cc_final: 0.7824 (ptt-90) REVERT: K 234 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7027 (tt0) REVERT: L 78 ARG cc_start: 0.8453 (tpt90) cc_final: 0.7850 (tpt90) REVERT: L 111 ASN cc_start: 0.8689 (t0) cc_final: 0.8355 (t0) REVERT: L 203 LYS cc_start: 0.8151 (tppp) cc_final: 0.7744 (tptp) REVERT: L 233 MET cc_start: 0.8051 (tpp) cc_final: 0.7845 (tpt) REVERT: M 80 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7053 (tt) REVERT: M 199 MET cc_start: 0.7070 (tpt) cc_final: 0.6641 (tpp) REVERT: N 178 HIS cc_start: 0.8796 (t-90) cc_final: 0.8495 (t70) REVERT: N 199 MET cc_start: 0.7619 (tmm) cc_final: 0.7340 (tmm) outliers start: 17 outliers final: 12 residues processed: 196 average time/residue: 0.1083 time to fit residues: 27.4986 Evaluate side-chains 190 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 214 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102886 restraints weight = 10853.558| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.18 r_work: 0.2928 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9252 Z= 0.118 Angle : 0.531 8.498 12499 Z= 0.268 Chirality : 0.043 0.150 1443 Planarity : 0.004 0.041 1574 Dihedral : 4.643 49.349 1254 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.68 % Allowed : 11.10 % Favored : 87.22 % 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 are not related in a simple way. whole: 0.04 (0.24), residues: 1130 helix: 0.38 (0.21), residues: 608 sheet: -0.39 (0.41), residues: 130 loop : -0.15 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 81 TYR 0.014 0.001 TYR M 138 PHE 0.010 0.001 PHE L 105 TRP 0.009 0.002 TRP H 146 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9252) covalent geometry : angle 0.53095 (12499) hydrogen bonds : bond 0.03310 ( 454) hydrogen bonds : angle 4.06431 ( 1497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.230 Fit side-chains REVERT: H 81 ARG cc_start: 0.7798 (ptm-80) cc_final: 0.7453 (mtp-110) REVERT: H 166 MET cc_start: 0.8185 (mtt) cc_final: 0.7907 (mtp) REVERT: H 199 MET cc_start: 0.7278 (tmm) cc_final: 0.6717 (tpt) REVERT: H 233 MET cc_start: 0.8359 (tpp) cc_final: 0.8128 (tpp) REVERT: I 173 SER cc_start: 0.8399 (m) cc_final: 0.8149 (p) REVERT: I 228 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7449 (ptt90) REVERT: K 110 SER cc_start: 0.8401 (t) cc_final: 0.8089 (m) REVERT: K 199 MET cc_start: 0.7149 (tmm) cc_final: 0.6598 (tmm) REVERT: K 226 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7375 (mtm180) REVERT: K 228 ARG cc_start: 0.8293 (ptt90) cc_final: 0.7842 (ptt90) REVERT: K 234 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7208 (tt0) REVERT: L 78 ARG cc_start: 0.8522 (tpt90) cc_final: 0.7907 (tpt90) REVERT: L 111 ASN cc_start: 0.8823 (t0) cc_final: 0.8441 (t0) REVERT: L 203 LYS cc_start: 0.8005 (tppp) cc_final: 0.7633 (tptp) REVERT: M 80 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7004 (tt) REVERT: M 199 MET cc_start: 0.7114 (tpt) cc_final: 0.6675 (tpp) REVERT: M 211 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7941 (tttm) REVERT: N 199 MET cc_start: 0.7572 (tmm) cc_final: 0.7235 (tmm) outliers start: 17 outliers final: 12 residues processed: 199 average time/residue: 0.1084 time to fit residues: 27.9795 Evaluate side-chains 190 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 215 GLN N 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.127004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098260 restraints weight = 11001.867| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.30 r_work: 0.2869 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9252 Z= 0.171 Angle : 0.572 8.642 12499 Z= 0.287 Chirality : 0.046 0.247 1443 Planarity : 0.004 0.041 1574 Dihedral : 4.679 47.805 1254 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 12.19 % Favored : 85.03 % 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 are not related in a simple way. whole: 0.00 (0.24), residues: 1130 helix: 0.31 (0.20), residues: 609 sheet: -0.19 (0.41), residues: 129 loop : -0.16 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 83 TYR 0.017 0.002 TYR K 206 PHE 0.011 0.002 PHE J 238 TRP 0.010 0.002 TRP I 146 HIS 0.019 0.001 HIS N 178 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9252) covalent geometry : angle 0.57180 (12499) hydrogen bonds : bond 0.03672 ( 454) hydrogen bonds : angle 4.11072 ( 1497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.340 Fit side-chains REVERT: H 81 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7519 (mtp-110) REVERT: H 166 MET cc_start: 0.8289 (mtt) cc_final: 0.8017 (mtp) REVERT: H 199 MET cc_start: 0.7287 (tmm) cc_final: 0.6845 (tmm) REVERT: H 233 MET cc_start: 0.8486 (tpp) cc_final: 0.8237 (tpp) REVERT: I 81 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8100 (mtm110) REVERT: I 173 SER cc_start: 0.8466 (m) cc_final: 0.8189 (p) REVERT: I 228 ARG cc_start: 0.7747 (ptm160) cc_final: 0.7506 (ptt90) REVERT: K 110 SER cc_start: 0.8416 (t) cc_final: 0.8106 (m) REVERT: K 111 ASN cc_start: 0.8223 (m110) cc_final: 0.7972 (t0) REVERT: K 166 MET cc_start: 0.8150 (mtp) cc_final: 0.7948 (mtp) REVERT: K 199 MET cc_start: 0.7206 (tmm) cc_final: 0.6624 (tmm) REVERT: K 214 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8077 (mmtm) REVERT: K 226 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7356 (mtm180) REVERT: K 228 ARG cc_start: 0.8349 (ptt90) cc_final: 0.7855 (ptt90) REVERT: K 234 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7215 (tt0) REVERT: L 78 ARG cc_start: 0.8544 (tpt90) cc_final: 0.7988 (tpt90) REVERT: L 111 ASN cc_start: 0.8910 (t0) cc_final: 0.8483 (t0) REVERT: L 203 LYS cc_start: 0.8127 (tppp) cc_final: 0.7765 (tptp) REVERT: M 80 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.6977 (tt) REVERT: M 104 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7238 (mm) REVERT: M 211 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8069 (tttm) REVERT: N 199 MET cc_start: 0.7586 (tmm) cc_final: 0.7236 (tmm) outliers start: 28 outliers final: 23 residues processed: 204 average time/residue: 0.1124 time to fit residues: 29.6904 Evaluate side-chains 207 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 178 HIS Chi-restraints excluded: chain N residue 233 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 ASN L 215 GLN N 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132161 restraints weight = 9774.228| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.54 r_work: 0.3507 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9252 Z= 0.149 Angle : 0.548 8.651 12499 Z= 0.275 Chirality : 0.044 0.167 1443 Planarity : 0.004 0.041 1574 Dihedral : 4.626 48.716 1254 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.68 % Allowed : 13.38 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1130 helix: 0.44 (0.21), residues: 609 sheet: -0.01 (0.41), residues: 127 loop : -0.23 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 83 TYR 0.020 0.001 TYR K 206 PHE 0.010 0.001 PHE J 238 TRP 0.011 0.002 TRP I 146 HIS 0.013 0.001 HIS N 178 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9252) covalent geometry : angle 0.54835 (12499) hydrogen bonds : bond 0.03441 ( 454) hydrogen bonds : angle 4.00214 ( 1497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.341 Fit side-chains REVERT: H 81 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7497 (mtp-110) REVERT: H 166 MET cc_start: 0.8158 (mtt) cc_final: 0.7916 (mtp) REVERT: H 199 MET cc_start: 0.7190 (tmm) cc_final: 0.6788 (tpt) REVERT: H 233 MET cc_start: 0.8585 (tpp) cc_final: 0.8374 (tpp) REVERT: I 81 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7987 (mtm110) REVERT: I 173 SER cc_start: 0.8491 (m) cc_final: 0.8218 (p) REVERT: I 228 ARG cc_start: 0.7781 (ptm160) cc_final: 0.7569 (ptt90) REVERT: K 110 SER cc_start: 0.8718 (t) cc_final: 0.8458 (m) REVERT: K 154 MET cc_start: 0.8134 (mmm) cc_final: 0.7825 (mmm) REVERT: K 199 MET cc_start: 0.7467 (tmm) cc_final: 0.6885 (tmm) REVERT: K 214 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8396 (mmtm) REVERT: K 226 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7601 (mtm180) REVERT: K 228 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7746 (ptt90) REVERT: K 234 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7412 (tt0) REVERT: L 78 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8291 (tpt90) REVERT: L 111 ASN cc_start: 0.8809 (t0) cc_final: 0.8333 (t0) REVERT: L 203 LYS cc_start: 0.8549 (tppp) cc_final: 0.8203 (tptp) REVERT: M 80 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7196 (tt) REVERT: M 104 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (mm) REVERT: M 211 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8259 (tttm) REVERT: N 199 MET cc_start: 0.7782 (tmm) cc_final: 0.7501 (tmm) outliers start: 27 outliers final: 20 residues processed: 202 average time/residue: 0.1151 time to fit residues: 29.7505 Evaluate side-chains 201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 233 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130703 restraints weight = 9812.657| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.56 r_work: 0.3486 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9252 Z= 0.170 Angle : 0.562 8.705 12499 Z= 0.282 Chirality : 0.045 0.152 1443 Planarity : 0.004 0.040 1574 Dihedral : 4.645 48.419 1254 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.07 % Allowed : 13.08 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1130 helix: 0.41 (0.21), residues: 609 sheet: -0.03 (0.41), residues: 128 loop : -0.23 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 83 TYR 0.018 0.001 TYR K 206 PHE 0.011 0.002 PHE J 238 TRP 0.012 0.002 TRP I 146 HIS 0.007 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9252) covalent geometry : angle 0.56195 (12499) hydrogen bonds : bond 0.03562 ( 454) hydrogen bonds : angle 4.03253 ( 1497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.245 Fit side-chains REVERT: H 81 ARG cc_start: 0.7963 (ptm-80) cc_final: 0.7469 (mtp-110) REVERT: H 166 MET cc_start: 0.8164 (mtt) cc_final: 0.7917 (mtp) REVERT: H 199 MET cc_start: 0.7135 (tmm) cc_final: 0.6786 (tpt) REVERT: H 233 MET cc_start: 0.8613 (tpp) cc_final: 0.8400 (tpp) REVERT: I 81 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8013 (mtm110) REVERT: I 199 MET cc_start: 0.7900 (tmm) cc_final: 0.7646 (tmm) REVERT: K 109 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7726 (mt-10) REVERT: K 110 SER cc_start: 0.8725 (t) cc_final: 0.8451 (m) REVERT: K 199 MET cc_start: 0.7451 (tmm) cc_final: 0.6857 (tmm) REVERT: K 214 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8413 (mmtm) REVERT: K 226 ARG cc_start: 0.8284 (mtm180) cc_final: 0.7862 (mtm180) REVERT: K 228 ARG cc_start: 0.8248 (ptt90) cc_final: 0.7803 (ptt90) REVERT: K 234 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7405 (tt0) REVERT: L 78 ARG cc_start: 0.8731 (tpt90) cc_final: 0.8269 (tpt90) REVERT: L 111 ASN cc_start: 0.8822 (t0) cc_final: 0.8355 (t0) REVERT: L 203 LYS cc_start: 0.8569 (tppp) cc_final: 0.8228 (tptp) REVERT: L 227 ASP cc_start: 0.8620 (t0) cc_final: 0.8338 (t0) REVERT: M 80 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7194 (tt) REVERT: M 104 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7830 (mm) REVERT: M 211 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8260 (tttm) REVERT: N 199 MET cc_start: 0.7733 (tmm) cc_final: 0.7451 (tmm) outliers start: 31 outliers final: 24 residues processed: 198 average time/residue: 0.1205 time to fit residues: 30.8993 Evaluate side-chains 200 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 233 MET Chi-restraints excluded: chain N residue 243 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 ASN K 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131332 restraints weight = 9729.758| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.55 r_work: 0.3489 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9252 Z= 0.154 Angle : 0.553 8.698 12499 Z= 0.276 Chirality : 0.045 0.152 1443 Planarity : 0.004 0.040 1574 Dihedral : 4.605 49.068 1254 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.07 % Allowed : 13.28 % Favored : 83.65 % 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 are not related in a simple way. whole: 0.18 (0.24), residues: 1130 helix: 0.50 (0.21), residues: 609 sheet: 0.09 (0.41), residues: 127 loop : -0.25 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 83 TYR 0.021 0.001 TYR K 206 PHE 0.009 0.001 PHE J 238 TRP 0.013 0.002 TRP I 146 HIS 0.007 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9252) covalent geometry : angle 0.55289 (12499) hydrogen bonds : bond 0.03413 ( 454) hydrogen bonds : angle 3.96741 ( 1497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: H 81 ARG cc_start: 0.7992 (ptm-80) cc_final: 0.7474 (mtp-110) REVERT: H 166 MET cc_start: 0.8190 (mtt) cc_final: 0.7953 (mtp) REVERT: H 199 MET cc_start: 0.7097 (tmm) cc_final: 0.6727 (tmm) REVERT: H 233 MET cc_start: 0.8612 (tpp) cc_final: 0.8389 (tpp) REVERT: I 81 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8002 (mtm110) REVERT: K 109 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7770 (mt-10) REVERT: K 110 SER cc_start: 0.8718 (t) cc_final: 0.8422 (m) REVERT: K 154 MET cc_start: 0.8111 (mmm) cc_final: 0.7641 (mmm) REVERT: K 199 MET cc_start: 0.7312 (tmm) cc_final: 0.6764 (tmm) REVERT: K 214 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8404 (mmtm) REVERT: K 226 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7832 (mtm180) REVERT: K 228 ARG cc_start: 0.8246 (ptt90) cc_final: 0.7772 (ptt90) REVERT: K 234 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7385 (tt0) REVERT: L 78 ARG cc_start: 0.8742 (tpt90) cc_final: 0.8291 (tpt90) REVERT: L 111 ASN cc_start: 0.8828 (t0) cc_final: 0.8386 (t0) REVERT: L 203 LYS cc_start: 0.8503 (tppp) cc_final: 0.8160 (tptp) REVERT: L 227 ASP cc_start: 0.8661 (t0) cc_final: 0.8334 (t0) REVERT: M 80 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7192 (tt) REVERT: M 104 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7815 (mm) REVERT: M 134 ASP cc_start: 0.7703 (t70) cc_final: 0.7423 (m-30) REVERT: M 211 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8265 (tttm) REVERT: N 109 GLU cc_start: 0.6540 (tt0) cc_final: 0.6307 (mt-10) REVERT: N 199 MET cc_start: 0.7737 (tmm) cc_final: 0.7452 (tmm) outliers start: 31 outliers final: 25 residues processed: 200 average time/residue: 0.1164 time to fit residues: 29.9196 Evaluate side-chains 203 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 233 MET Chi-restraints excluded: chain N residue 243 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 215 GLN K 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132636 restraints weight = 9688.330| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.54 r_work: 0.3512 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9252 Z= 0.134 Angle : 0.539 8.671 12499 Z= 0.268 Chirality : 0.044 0.157 1443 Planarity : 0.004 0.040 1574 Dihedral : 4.522 49.747 1254 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.97 % Allowed : 13.88 % Favored : 83.15 % 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 are not related in a simple way. whole: 0.29 (0.24), residues: 1130 helix: 0.62 (0.21), residues: 610 sheet: 0.14 (0.41), residues: 126 loop : -0.26 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 83 TYR 0.022 0.001 TYR K 206 PHE 0.012 0.001 PHE J 238 TRP 0.012 0.002 TRP I 146 HIS 0.007 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9252) covalent geometry : angle 0.53944 (12499) hydrogen bonds : bond 0.03209 ( 454) hydrogen bonds : angle 3.88425 ( 1497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: H 81 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7489 (mtp-110) REVERT: H 82 GLU cc_start: 0.7543 (pt0) cc_final: 0.7279 (tm-30) REVERT: H 104 LEU cc_start: 0.7240 (pp) cc_final: 0.6907 (mt) REVERT: H 166 MET cc_start: 0.8183 (mtt) cc_final: 0.7974 (mtp) REVERT: H 199 MET cc_start: 0.7091 (tmm) cc_final: 0.6691 (tmm) REVERT: H 233 MET cc_start: 0.8590 (tpp) cc_final: 0.8379 (tpp) REVERT: I 81 ARG cc_start: 0.8311 (mtp-110) cc_final: 0.7988 (mtm110) REVERT: I 199 MET cc_start: 0.7904 (tmm) cc_final: 0.7559 (tpp) REVERT: K 109 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7790 (mt-10) REVERT: K 110 SER cc_start: 0.8673 (t) cc_final: 0.8367 (m) REVERT: K 154 MET cc_start: 0.8046 (mmm) cc_final: 0.7606 (mmm) REVERT: K 199 MET cc_start: 0.7229 (tmm) cc_final: 0.6661 (tmm) REVERT: K 214 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8414 (mmtm) REVERT: K 226 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7818 (mtm180) REVERT: K 228 ARG cc_start: 0.8265 (ptt90) cc_final: 0.7776 (ptt90) REVERT: K 234 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7364 (tt0) REVERT: L 78 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8281 (tpt90) REVERT: L 111 ASN cc_start: 0.8823 (t0) cc_final: 0.8387 (t0) REVERT: L 203 LYS cc_start: 0.8440 (tppp) cc_final: 0.8107 (tptp) REVERT: M 80 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7192 (tt) REVERT: M 104 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7789 (mm) REVERT: M 134 ASP cc_start: 0.7674 (t70) cc_final: 0.7452 (m-30) REVERT: M 211 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8271 (tttm) REVERT: N 109 GLU cc_start: 0.6499 (tt0) cc_final: 0.6256 (mt-10) REVERT: N 199 MET cc_start: 0.7726 (tmm) cc_final: 0.7466 (tmm) outliers start: 30 outliers final: 24 residues processed: 204 average time/residue: 0.1226 time to fit residues: 32.1775 Evaluate side-chains 203 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 233 MET Chi-restraints excluded: chain N residue 243 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 ASN J 215 GLN K 111 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135309 restraints weight = 9588.496| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.53 r_work: 0.3543 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9252 Z= 0.111 Angle : 0.534 8.560 12499 Z= 0.264 Chirality : 0.043 0.245 1443 Planarity : 0.004 0.039 1574 Dihedral : 4.438 50.901 1254 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 14.77 % Favored : 82.76 % 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 are not related in a simple way. whole: 0.48 (0.25), residues: 1130 helix: 0.82 (0.21), residues: 610 sheet: 0.19 (0.41), residues: 126 loop : -0.25 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 83 TYR 0.030 0.001 TYR K 206 PHE 0.007 0.001 PHE J 238 TRP 0.012 0.002 TRP H 146 HIS 0.015 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9252) covalent geometry : angle 0.53361 (12499) hydrogen bonds : bond 0.02966 ( 454) hydrogen bonds : angle 3.78558 ( 1497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: H 81 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7475 (mtp-110) REVERT: H 104 LEU cc_start: 0.7187 (pp) cc_final: 0.6929 (mt) REVERT: H 199 MET cc_start: 0.7031 (tmm) cc_final: 0.6734 (tpt) REVERT: H 233 MET cc_start: 0.8581 (tpp) cc_final: 0.8368 (tpp) REVERT: I 81 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.7970 (mtm110) REVERT: I 199 MET cc_start: 0.7825 (tmm) cc_final: 0.7476 (tpp) REVERT: K 109 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7718 (mt-10) REVERT: K 154 MET cc_start: 0.8075 (mmm) cc_final: 0.7574 (mmm) REVERT: K 199 MET cc_start: 0.7090 (tmm) cc_final: 0.6525 (tmm) REVERT: K 214 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8375 (mmtm) REVERT: K 226 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7816 (mtm180) REVERT: K 228 ARG cc_start: 0.8280 (ptt90) cc_final: 0.7797 (ptt90) REVERT: K 234 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7416 (tt0) REVERT: L 78 ARG cc_start: 0.8696 (tpt90) cc_final: 0.8247 (tpt90) REVERT: L 111 ASN cc_start: 0.8789 (t0) cc_final: 0.8340 (t0) REVERT: L 203 LYS cc_start: 0.8383 (tppp) cc_final: 0.8127 (tptp) REVERT: M 80 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7184 (tt) REVERT: M 104 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7800 (mm) REVERT: N 109 GLU cc_start: 0.6469 (tt0) cc_final: 0.6213 (mt-10) REVERT: N 199 MET cc_start: 0.7693 (tmm) cc_final: 0.7437 (tmm) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 0.1243 time to fit residues: 31.5174 Evaluate side-chains 193 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 154 MET Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain N residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 215 GLN K 111 ASN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133032 restraints weight = 9566.831| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.54 r_work: 0.3512 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9252 Z= 0.142 Angle : 0.564 10.021 12499 Z= 0.283 Chirality : 0.044 0.237 1443 Planarity : 0.004 0.041 1574 Dihedral : 4.456 49.990 1254 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.68 % Allowed : 14.97 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1130 helix: 0.77 (0.21), residues: 610 sheet: 0.16 (0.41), residues: 126 loop : -0.27 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 83 TYR 0.017 0.001 TYR K 206 PHE 0.007 0.001 PHE J 238 TRP 0.015 0.002 TRP N 146 HIS 0.013 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9252) covalent geometry : angle 0.56441 (12499) hydrogen bonds : bond 0.03158 ( 454) hydrogen bonds : angle 3.83931 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1966.06 seconds wall clock time: 34 minutes 18.79 seconds (2058.79 seconds total)