Starting phenix.real_space_refine on Wed Mar 12 09:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2025/7nnu_12484.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 36 5.16 5 C 5004 2.51 5 N 1266 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2137 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2131 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2100 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 5.57, per 1000 atoms: 0.72 Number of scatterers: 7724 At special positions: 0 Unit cell: (87.894, 105.627, 100.23, 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 36 16.00 O 1418 8.00 N 1266 7.00 C 5004 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 63.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 131 Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.022A pdb=" N ALA A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.188A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.578A pdb=" N GLN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.772A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.098A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.578A pdb=" N LEU A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 4.119A pdb=" N ASN B 54 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.541A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.538A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.562A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.694A pdb=" N LEU B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 177 through 194 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.737A pdb=" N LEU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 43 through 76 removed outlier: 3.930A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 82 through 101 removed outlier: 3.769A pdb=" N THR C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 147 through 150 removed outlier: 3.652A pdb=" N MET C 150 " --> pdb=" O LEU C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 151 through 172 removed outlier: 3.869A pdb=" N ILE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.705A pdb=" N ARG D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.581A pdb=" N LEU D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 3.731A pdb=" N GLY D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.036A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 102 through 129 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 152 through 184 Proline residue: D 168 - end of helix removed outlier: 3.714A pdb=" N ARG D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'D' and resid 200 through 225 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.843A pdb=" N VAL D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 6.791A pdb=" N SER A 24 " --> pdb=" O HIS A 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 10 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 26 " --> pdb=" O PHE A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.581A pdb=" N TRP A 35 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A 214 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 37 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU A 216 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 39 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 30 removed outlier: 6.198A pdb=" N ASP B 24 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 9 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 8 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 61 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.364A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 36 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 35 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 216 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA B 37 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 218 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 39 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 34 445 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2334 1.34 - 1.46: 1497 1.46 - 1.58: 3951 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 7850 Sorted by residual: bond pdb=" CG1 ILE C 74 " pdb=" CD1 ILE C 74 " ideal model delta sigma weight residual 1.513 1.390 0.123 3.90e-02 6.57e+02 9.95e+00 bond pdb=" CG LEU D 164 " pdb=" CD1 LEU D 164 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CG LEU A 74 " pdb=" CD1 LEU A 74 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB PRO D 202 " pdb=" CG PRO D 202 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.61e+00 bond pdb=" CG PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 1.503 1.449 0.054 3.40e-02 8.65e+02 2.57e+00 ... (remaining 7845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10080 1.53 - 3.06: 425 3.06 - 4.60: 90 4.60 - 6.13: 21 6.13 - 7.66: 14 Bond angle restraints: 10630 Sorted by residual: angle pdb=" C PHE A 13 " pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C LYS A 190 " pdb=" N GLU A 191 " pdb=" CA GLU A 191 " ideal model delta sigma weight residual 122.56 116.69 5.87 1.72e+00 3.38e-01 1.16e+01 angle pdb=" CA TRP B 128 " pdb=" CB TRP B 128 " pdb=" CG TRP B 128 " ideal model delta sigma weight residual 113.60 107.44 6.16 1.90e+00 2.77e-01 1.05e+01 angle pdb=" N GLN A 273 " pdb=" CA GLN A 273 " pdb=" CB GLN A 273 " ideal model delta sigma weight residual 110.16 114.85 -4.69 1.48e+00 4.57e-01 1.00e+01 angle pdb=" CB GLN A 277 " pdb=" CG GLN A 277 " pdb=" CD GLN A 277 " ideal model delta sigma weight residual 112.60 117.84 -5.24 1.70e+00 3.46e-01 9.50e+00 ... (remaining 10625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 4148 17.08 - 34.15: 438 34.15 - 51.22: 65 51.22 - 68.30: 11 68.30 - 85.37: 8 Dihedral angle restraints: 4670 sinusoidal: 1861 harmonic: 2809 Sorted by residual: dihedral pdb=" CA GLY C 80 " pdb=" C GLY C 80 " pdb=" N PHE C 81 " pdb=" CA PHE C 81 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASP A 267 " pdb=" C ASP A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG D 184 " pdb=" C ARG D 184 " pdb=" N GLY D 185 " pdb=" CA GLY D 185 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1104 0.087 - 0.174: 120 0.174 - 0.261: 4 0.261 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CB ILE A 6 " pdb=" CA ILE A 6 " pdb=" CG1 ILE A 6 " pdb=" CG2 ILE A 6 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU A 191 " pdb=" N GLU A 191 " pdb=" C GLU A 191 " pdb=" CB GLU A 191 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1226 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 97 " -0.011 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE A 97 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 97 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 97 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 97 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 97 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 97 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 177 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 178 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 72 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO B 73 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " -0.039 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1738 2.78 - 3.31: 7290 3.31 - 3.84: 13828 3.84 - 4.37: 16660 4.37 - 4.90: 27732 Nonbonded interactions: 67248 Sorted by model distance: nonbonded pdb=" O VAL A 106 " pdb=" O HOH A 301 " model vdw 2.251 3.040 nonbonded pdb=" O LEU D 258 " pdb=" OG1 THR D 262 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP A 105 " pdb=" O HOH A 302 " model vdw 2.277 3.040 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 12 " pdb=" OD2 ASP A 60 " model vdw 2.315 3.040 ... (remaining 67243 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.007 0.123 7850 Z= 0.421 Angle : 0.794 7.660 10630 Z= 0.431 Chirality : 0.054 0.434 1229 Planarity : 0.007 0.071 1327 Dihedral : 14.015 85.373 2860 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 970 helix: -0.32 (0.20), residues: 570 sheet: 0.17 (0.63), residues: 61 loop : -0.45 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 128 HIS 0.004 0.001 HIS A 202 PHE 0.050 0.003 PHE A 97 TYR 0.016 0.002 TYR C 134 ARG 0.010 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.845 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.3578 time to fit residues: 230.5298 Evaluate side-chains 122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 220 GLN B 7 ASN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103863 restraints weight = 9627.309| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.65 r_work: 0.3033 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7850 Z= 0.202 Angle : 0.554 6.177 10630 Z= 0.295 Chirality : 0.043 0.147 1229 Planarity : 0.006 0.066 1327 Dihedral : 4.694 15.941 1038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 8.65 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 970 helix: 0.99 (0.22), residues: 563 sheet: -0.31 (0.59), residues: 73 loop : -0.22 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 128 HIS 0.002 0.001 HIS A 202 PHE 0.011 0.001 PHE C 55 TYR 0.012 0.001 TYR C 134 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: A 271 LEU cc_start: 0.8612 (tp) cc_final: 0.8320 (tt) REVERT: A 274 SER cc_start: 0.8188 (t) cc_final: 0.7465 (p) REVERT: A 275 LEU cc_start: 0.8808 (mt) cc_final: 0.8569 (mt) REVERT: B 7 ASN cc_start: 0.8161 (t0) cc_final: 0.7741 (t0) REVERT: B 256 LEU cc_start: 0.8119 (mp) cc_final: 0.7893 (mp) REVERT: C 33 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6829 (tttm) outliers start: 11 outliers final: 2 residues processed: 142 average time/residue: 1.2122 time to fit residues: 182.2598 Evaluate side-chains 131 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain C residue 33 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099800 restraints weight = 9715.904| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.69 r_work: 0.2985 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7850 Z= 0.281 Angle : 0.564 6.381 10630 Z= 0.297 Chirality : 0.045 0.148 1229 Planarity : 0.005 0.059 1327 Dihedral : 4.635 16.247 1038 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.16 % Allowed : 10.22 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 970 helix: 1.34 (0.22), residues: 563 sheet: -0.48 (0.63), residues: 62 loop : -0.11 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 128 HIS 0.002 0.001 HIS A 10 PHE 0.011 0.002 PHE B 35 TYR 0.015 0.002 TYR D 251 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: B 7 ASN cc_start: 0.8129 (t0) cc_final: 0.7699 (t0) REVERT: B 163 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: C 33 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.6950 (tttm) REVERT: C 168 SER cc_start: 0.8850 (m) cc_final: 0.8634 (p) REVERT: D 142 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8460 (mtt) REVERT: D 240 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7415 (mm-30) outliers start: 18 outliers final: 7 residues processed: 138 average time/residue: 1.8316 time to fit residues: 267.5916 Evaluate side-chains 135 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 91 GLN D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100891 restraints weight = 9626.395| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.69 r_work: 0.2995 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7850 Z= 0.208 Angle : 0.524 6.513 10630 Z= 0.276 Chirality : 0.043 0.148 1229 Planarity : 0.005 0.056 1327 Dihedral : 4.446 15.372 1038 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.64 % Allowed : 11.30 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 970 helix: 1.58 (0.22), residues: 566 sheet: -0.56 (0.59), residues: 73 loop : -0.07 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 128 HIS 0.002 0.001 HIS A 202 PHE 0.009 0.001 PHE A 231 TYR 0.014 0.001 TYR D 251 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.842 Fit side-chains REVERT: A 194 ASN cc_start: 0.8496 (t0) cc_final: 0.8041 (t0) REVERT: A 229 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: B 163 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: C 33 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6975 (tttm) REVERT: C 168 SER cc_start: 0.8861 (m) cc_final: 0.8646 (p) REVERT: D 142 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: D 240 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7401 (mm-30) outliers start: 22 outliers final: 7 residues processed: 144 average time/residue: 1.3271 time to fit residues: 202.4478 Evaluate side-chains 137 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS B 7 ASN C 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101331 restraints weight = 9524.757| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.68 r_work: 0.3003 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7850 Z= 0.215 Angle : 0.530 8.957 10630 Z= 0.277 Chirality : 0.044 0.157 1229 Planarity : 0.005 0.056 1327 Dihedral : 4.409 16.791 1038 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.52 % Allowed : 13.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 970 helix: 1.66 (0.22), residues: 566 sheet: -0.63 (0.58), residues: 73 loop : -0.12 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.008 0.001 PHE A 231 TYR 0.015 0.001 TYR D 251 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 194 ASN cc_start: 0.8497 (t0) cc_final: 0.8045 (t0) REVERT: A 229 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: B 106 ASP cc_start: 0.8463 (t0) cc_final: 0.8118 (t70) REVERT: B 163 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: B 169 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9122 (mp) REVERT: B 246 GLU cc_start: 0.7986 (mp0) cc_final: 0.7777 (mp0) REVERT: C 33 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.6993 (tttm) REVERT: C 168 SER cc_start: 0.8888 (m) cc_final: 0.8684 (p) REVERT: D 66 TRP cc_start: 0.7421 (t-100) cc_final: 0.6916 (t-100) REVERT: D 142 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: D 240 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7394 (mm-30) outliers start: 21 outliers final: 8 residues processed: 142 average time/residue: 1.3961 time to fit residues: 210.8025 Evaluate side-chains 139 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS B 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100798 restraints weight = 9553.864| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.69 r_work: 0.2995 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7850 Z= 0.232 Angle : 0.534 8.760 10630 Z= 0.281 Chirality : 0.044 0.144 1229 Planarity : 0.005 0.054 1327 Dihedral : 4.381 15.439 1038 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.64 % Allowed : 13.22 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 970 helix: 1.69 (0.22), residues: 566 sheet: -0.60 (0.58), residues: 73 loop : -0.07 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.009 0.001 PHE A 231 TYR 0.015 0.002 TYR D 251 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.888 Fit side-chains REVERT: A 194 ASN cc_start: 0.8528 (t0) cc_final: 0.8076 (t0) REVERT: A 229 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 163 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 246 GLU cc_start: 0.7930 (mp0) cc_final: 0.7711 (mp0) REVERT: C 33 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7016 (tttm) REVERT: C 77 ASN cc_start: 0.6717 (t0) cc_final: 0.6446 (t0) REVERT: D 66 TRP cc_start: 0.7427 (t-100) cc_final: 0.6957 (t-100) REVERT: D 142 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: D 240 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7388 (mm-30) outliers start: 22 outliers final: 8 residues processed: 140 average time/residue: 1.1593 time to fit residues: 172.1123 Evaluate side-chains 139 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS B 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102281 restraints weight = 9711.187| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.61 r_work: 0.3014 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7850 Z= 0.276 Angle : 0.563 9.228 10630 Z= 0.292 Chirality : 0.045 0.144 1229 Planarity : 0.005 0.054 1327 Dihedral : 4.463 15.495 1038 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 15.02 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 970 helix: 1.67 (0.22), residues: 566 sheet: -0.60 (0.61), residues: 62 loop : 0.02 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.010 0.001 PHE A 231 TYR 0.016 0.002 TYR D 251 ARG 0.009 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.856 Fit side-chains REVERT: A 194 ASN cc_start: 0.8512 (t0) cc_final: 0.8065 (t0) REVERT: A 229 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: B 163 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: B 246 GLU cc_start: 0.7957 (mp0) cc_final: 0.7738 (mp0) REVERT: C 33 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.6987 (tttm) REVERT: C 77 ASN cc_start: 0.6988 (t0) cc_final: 0.6677 (t0) REVERT: D 142 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8396 (mtt) REVERT: D 240 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7422 (mm-30) outliers start: 19 outliers final: 7 residues processed: 140 average time/residue: 1.1463 time to fit residues: 170.1781 Evaluate side-chains 136 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103453 restraints weight = 9681.710| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.67 r_work: 0.3022 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7850 Z= 0.169 Angle : 0.509 9.220 10630 Z= 0.265 Chirality : 0.042 0.142 1229 Planarity : 0.005 0.054 1327 Dihedral : 4.227 14.204 1038 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 15.26 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 970 helix: 1.88 (0.22), residues: 565 sheet: -0.51 (0.59), residues: 73 loop : -0.05 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 276 HIS 0.002 0.000 HIS A 202 PHE 0.008 0.001 PHE C 61 TYR 0.012 0.001 TYR D 251 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.904 Fit side-chains REVERT: A 194 ASN cc_start: 0.8511 (t0) cc_final: 0.8087 (t0) REVERT: A 229 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: B 246 GLU cc_start: 0.7836 (mp0) cc_final: 0.7609 (mp0) REVERT: C 77 ASN cc_start: 0.6771 (t0) cc_final: 0.6469 (t0) REVERT: D 66 TRP cc_start: 0.7435 (t-100) cc_final: 0.6705 (t-100) REVERT: D 148 LEU cc_start: 0.7205 (pp) cc_final: 0.6751 (mm) REVERT: D 240 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7499 (mm-30) outliers start: 19 outliers final: 6 residues processed: 145 average time/residue: 1.2044 time to fit residues: 185.0399 Evaluate side-chains 134 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 240 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN A 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.101227 restraints weight = 9835.052| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.73 r_work: 0.2999 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7850 Z= 0.238 Angle : 0.544 8.912 10630 Z= 0.283 Chirality : 0.044 0.141 1229 Planarity : 0.005 0.052 1327 Dihedral : 4.311 15.668 1038 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 16.23 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 970 helix: 1.83 (0.22), residues: 565 sheet: -0.49 (0.58), residues: 73 loop : 0.01 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.008 0.001 PHE C 162 TYR 0.019 0.002 TYR C 53 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.855 Fit side-chains REVERT: A 194 ASN cc_start: 0.8512 (t0) cc_final: 0.8090 (t0) REVERT: A 229 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: B 106 ASP cc_start: 0.8493 (t0) cc_final: 0.8125 (t70) REVERT: B 135 LYS cc_start: 0.8025 (mptt) cc_final: 0.6950 (mmmt) REVERT: B 246 GLU cc_start: 0.7884 (mp0) cc_final: 0.7628 (mp0) REVERT: C 77 ASN cc_start: 0.6942 (t0) cc_final: 0.6625 (t0) REVERT: D 66 TRP cc_start: 0.7381 (t-100) cc_final: 0.6857 (t-100) REVERT: D 142 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8445 (mtt) REVERT: D 240 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (mm-30) outliers start: 14 outliers final: 10 residues processed: 136 average time/residue: 1.4675 time to fit residues: 210.8978 Evaluate side-chains 140 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 0.0030 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN A 163 GLN A 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103564 restraints weight = 9678.351| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.66 r_work: 0.3020 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7850 Z= 0.176 Angle : 0.518 9.033 10630 Z= 0.271 Chirality : 0.043 0.140 1229 Planarity : 0.005 0.053 1327 Dihedral : 4.216 15.221 1038 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.92 % Allowed : 16.23 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 970 helix: 1.91 (0.22), residues: 565 sheet: -0.50 (0.60), residues: 73 loop : -0.02 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 276 HIS 0.003 0.000 HIS A 202 PHE 0.008 0.001 PHE C 61 TYR 0.013 0.001 TYR D 251 ARG 0.008 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.910 Fit side-chains REVERT: A 194 ASN cc_start: 0.8529 (t0) cc_final: 0.8113 (t0) REVERT: A 229 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: A 269 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: B 135 LYS cc_start: 0.8038 (mptt) cc_final: 0.6970 (mmmt) REVERT: B 246 GLU cc_start: 0.7788 (mp0) cc_final: 0.7544 (mp0) REVERT: C 77 ASN cc_start: 0.6817 (t0) cc_final: 0.6489 (t0) REVERT: D 66 TRP cc_start: 0.7436 (t-100) cc_final: 0.6708 (t-100) REVERT: D 240 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7491 (mm-30) outliers start: 16 outliers final: 9 residues processed: 139 average time/residue: 1.1598 time to fit residues: 170.9122 Evaluate side-chains 140 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN A 202 HIS C 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100906 restraints weight = 9757.662| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.72 r_work: 0.3004 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7850 Z= 0.253 Angle : 0.554 8.878 10630 Z= 0.288 Chirality : 0.044 0.140 1229 Planarity : 0.005 0.053 1327 Dihedral : 4.328 15.398 1038 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 16.23 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 970 helix: 1.82 (0.22), residues: 565 sheet: -0.43 (0.59), residues: 73 loop : -0.00 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.009 0.001 PHE C 162 TYR 0.023 0.002 TYR C 53 ARG 0.007 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6622.18 seconds wall clock time: 117 minutes 58.47 seconds (7078.47 seconds total)