Starting phenix.real_space_refine on Thu Jul 2 08:52:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmp_16120/07_2026/8bmp_16120.map" } resolution = 3.2 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= 0.009 sd= 0.103 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5052 2.51 5 N 1283 2.21 5 O 1417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7794 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2130 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2183 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} 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: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2101 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.28, per 1000 atoms: 0.16 Number of scatterers: 7794 At special positions: 0 Unit cell: (83.804, 85.848, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 5 15.00 Mg 1 11.99 O 1417 8.00 N 1283 7.00 C 5052 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: 0.52 Conformation dependent library (CDL) restraints added in 278.4 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 60.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.598A pdb=" N VAL A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 removed outlier: 4.635A pdb=" N GLY A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.847A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.037A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.430A pdb=" N ALA A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.934A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.766A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.521A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.244A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.694A pdb=" N PHE B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 177 through 194 Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'C' and resid 12 through 30 Processing helix chain 'C' and resid 43 through 75 removed outlier: 3.895A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 57 - end of helix removed outlier: 3.541A pdb=" N ASP C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 removed outlier: 4.045A 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 144 Processing helix chain 'C' and resid 145 through 152 removed outlier: 3.633A pdb=" N GLU C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 172 removed outlier: 4.159A pdb=" N VAL C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 36 removed outlier: 3.894A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.201A 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 103 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 183 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 191 through 199 removed outlier: 4.191A pdb=" N LYS D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 225 removed outlier: 3.964A pdb=" N MET D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.701A pdb=" N VAL D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.345A pdb=" N SER A 66 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.391A pdb=" N ILE A 165 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE A 200 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 167 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA A 37 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU A 216 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 39 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 223 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP A 217 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 30 removed outlier: 6.311A pdb=" N TYR B 10 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP B 24 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL B 8 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU B 26 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU B 6 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE B 28 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS B 4 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.528A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE B 35 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU B 216 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 37 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 218 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 39 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 225 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.191A 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 35 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.598A pdb=" N LEU D 101 " --> pdb=" O TYR D 93 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1221 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: 0.97 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2456 1.34 - 1.46: 1683 1.46 - 1.58: 3747 1.58 - 1.70: 7 1.70 - 1.81: 68 Bond restraints: 7961 Sorted by residual: bond pdb=" C VAL D 167 " pdb=" N PRO D 168 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.97e+00 bond pdb=" C4 ADP B 301 " pdb=" C5 ADP B 301 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA SER A 27 " pdb=" C SER A 27 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.08e-02 8.57e+03 9.27e-01 bond pdb=" CA THR C 152 " pdb=" C THR C 152 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.26e-02 6.30e+03 7.83e-01 bond pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.74e-01 ... (remaining 7956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 10416 1.45 - 2.90: 298 2.90 - 4.35: 58 4.35 - 5.80: 23 5.80 - 7.25: 2 Bond angle restraints: 10797 Sorted by residual: angle pdb=" N ILE D 98 " pdb=" CA ILE D 98 " pdb=" C ILE D 98 " ideal model delta sigma weight residual 113.71 110.15 3.56 9.50e-01 1.11e+00 1.40e+01 angle pdb=" N GLU B 6 " pdb=" CA GLU B 6 " pdb=" C GLU B 6 " ideal model delta sigma weight residual 109.94 104.74 5.20 1.57e+00 4.06e-01 1.10e+01 angle pdb=" C ASP A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta sigma weight residual 120.63 125.93 -5.30 1.61e+00 3.86e-01 1.08e+01 angle pdb=" N ASP A 268 " pdb=" CA ASP A 268 " pdb=" C ASP A 268 " ideal model delta sigma weight residual 112.34 116.45 -4.11 1.30e+00 5.92e-01 1.00e+01 angle pdb=" N GLY C 35 " pdb=" CA GLY C 35 " pdb=" C GLY C 35 " ideal model delta sigma weight residual 110.38 114.71 -4.33 1.42e+00 4.96e-01 9.30e+00 ... (remaining 10792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 4601 31.01 - 62.02: 107 62.02 - 93.03: 6 93.03 - 124.04: 0 124.04 - 155.04: 2 Dihedral angle restraints: 4716 sinusoidal: 1887 harmonic: 2829 Sorted by residual: dihedral pdb=" O2A ADP B 301 " pdb=" O3A ADP B 301 " pdb=" PA ADP B 301 " pdb=" PB ADP B 301 " ideal model delta sinusoidal sigma weight residual -60.00 95.05 -155.04 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O1B ADP B 301 " pdb=" O3A ADP B 301 " pdb=" PB ADP B 301 " pdb=" PA ADP B 301 " ideal model delta sinusoidal sigma weight residual -60.00 74.33 -134.34 1 2.00e+01 2.50e-03 4.08e+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 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 692 0.029 - 0.057: 339 0.057 - 0.086: 127 0.086 - 0.114: 67 0.114 - 0.143: 18 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CA THR C 152 " pdb=" N THR C 152 " pdb=" C THR C 152 " pdb=" CB THR C 152 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE C 123 " pdb=" N ILE C 123 " pdb=" C ILE C 123 " pdb=" CB ILE C 123 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1240 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 270 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 271 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 93 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 252 " 0.007 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE B 252 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 252 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 252 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 252 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 252 " 0.001 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1572 2.78 - 3.31: 7626 3.31 - 3.84: 12653 3.84 - 4.37: 15098 4.37 - 4.90: 26060 Nonbonded interactions: 63009 Sorted by model distance: nonbonded pdb=" O GLU D 104 " pdb=" ND2 ASN D 108 " model vdw 2.246 3.120 nonbonded pdb=" OD2 ASP A 61 " pdb=" NZ LYS A 64 " model vdw 2.297 3.120 nonbonded pdb=" OG1 THR A 101 " pdb=" OD1 ASP A 104 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP D 172 " pdb=" NZ LYS D 176 " model vdw 2.351 3.120 nonbonded pdb=" OD1 ASP A 266 " pdb=" N ASP A 267 " model vdw 2.378 3.120 ... (remaining 63004 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: 0.920 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.980 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 0.035 7961 Z= 0.151 Angle : 0.636 7.246 10797 Z= 0.351 Chirality : 0.043 0.143 1243 Planarity : 0.004 0.050 1341 Dihedral : 13.724 155.045 2894 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 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: 0.66 (0.27), residues: 979 helix: 1.09 (0.22), residues: 571 sheet: 0.87 (0.71), residues: 62 loop : -0.65 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 235 TYR 0.012 0.001 TYR D 44 PHE 0.024 0.001 PHE B 252 TRP 0.021 0.001 TRP A 276 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7961) covalent geometry : angle 0.63606 / 0.35 (10797) hydrogen bonds : bond 0.14881 / 10.08 ( 425) hydrogen bonds : angle 5.60249 / 3.90 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.180 Fit side-chains REVERT: A 184 ASP cc_start: 0.7837 (m-30) cc_final: 0.7391 (m-30) REVERT: C 129 TRP cc_start: 0.8101 (m-10) cc_final: 0.7843 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0763 time to fit residues: 10.8989 Evaluate side-chains 96 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110094 restraints weight = 10194.519| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.04 r_work: 0.3158 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7961 Z= 0.112 Angle : 0.546 6.722 10797 Z= 0.272 Chirality : 0.042 0.147 1243 Planarity : 0.004 0.038 1341 Dihedral : 7.702 159.864 1060 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.48 % Allowed : 5.38 % Favored : 94.15 % 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: 1.25 (0.27), residues: 979 helix: 1.68 (0.22), residues: 573 sheet: 0.47 (0.68), residues: 62 loop : -0.50 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.013 0.001 TYR D 251 PHE 0.015 0.001 PHE B 252 TRP 0.011 0.001 TRP B 128 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7961) covalent geometry : angle 0.54599 / 0.27 (10797) hydrogen bonds : bond 0.04136 / 2.83 ( 425) hydrogen bonds : angle 4.17528 / 2.92 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.234 Fit side-chains REVERT: A 184 ASP cc_start: 0.7941 (m-30) cc_final: 0.7430 (m-30) REVERT: C 129 TRP cc_start: 0.7656 (m-10) cc_final: 0.7269 (m-10) REVERT: C 138 PHE cc_start: 0.7638 (t80) cc_final: 0.7370 (t80) REVERT: D 108 ASN cc_start: 0.7942 (m-40) cc_final: 0.7514 (m-40) REVERT: D 155 MET cc_start: 0.8029 (mtm) cc_final: 0.7754 (mtt) REVERT: D 203 MET cc_start: 0.8269 (ttm) cc_final: 0.7872 (ttm) outliers start: 4 outliers final: 1 residues processed: 104 average time/residue: 0.0749 time to fit residues: 10.6214 Evaluate side-chains 100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107104 restraints weight = 10178.594| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.06 r_work: 0.3108 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7961 Z= 0.169 Angle : 0.571 6.902 10797 Z= 0.284 Chirality : 0.044 0.150 1243 Planarity : 0.004 0.039 1341 Dihedral : 7.768 169.007 1060 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 6.33 % Favored : 92.83 % 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: 1.20 (0.27), residues: 979 helix: 1.69 (0.22), residues: 570 sheet: 0.06 (0.67), residues: 62 loop : -0.53 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.014 0.002 TYR D 251 PHE 0.013 0.001 PHE D 86 TRP 0.013 0.001 TRP B 128 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 7961) covalent geometry : angle 0.57098 / 0.28 (10797) hydrogen bonds : bond 0.04366 / 3.01 ( 425) hydrogen bonds : angle 4.09846 / 2.88 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.204 Fit side-chains REVERT: A 184 ASP cc_start: 0.7937 (m-30) cc_final: 0.7421 (m-30) REVERT: A 266 ASP cc_start: 0.7049 (t0) cc_final: 0.6417 (m-30) REVERT: C 129 TRP cc_start: 0.7824 (m-10) cc_final: 0.7376 (m-10) REVERT: C 138 PHE cc_start: 0.7657 (t80) cc_final: 0.7393 (t80) REVERT: D 108 ASN cc_start: 0.7846 (m-40) cc_final: 0.7608 (m-40) outliers start: 7 outliers final: 2 residues processed: 102 average time/residue: 0.0876 time to fit residues: 11.8758 Evaluate side-chains 101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107248 restraints weight = 10351.728| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.06 r_work: 0.3112 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7961 Z= 0.153 Angle : 0.551 6.771 10797 Z= 0.273 Chirality : 0.043 0.147 1243 Planarity : 0.003 0.038 1341 Dihedral : 7.801 174.393 1060 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.72 % Allowed : 8.84 % Favored : 90.44 % 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: 1.16 (0.27), residues: 979 helix: 1.71 (0.22), residues: 570 sheet: -0.39 (0.65), residues: 63 loop : -0.54 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 249 TYR 0.013 0.001 TYR D 251 PHE 0.018 0.001 PHE B 252 TRP 0.012 0.001 TRP B 128 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 ( 7961) covalent geometry : angle 0.55056 / 0.27 (10797) hydrogen bonds : bond 0.04085 / 2.82 ( 425) hydrogen bonds : angle 4.04382 / 2.85 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.213 Fit side-chains REVERT: A 184 ASP cc_start: 0.7961 (m-30) cc_final: 0.7459 (m-30) REVERT: A 266 ASP cc_start: 0.6902 (t0) cc_final: 0.6243 (m-30) REVERT: C 129 TRP cc_start: 0.7799 (m-10) cc_final: 0.7466 (m-10) REVERT: C 138 PHE cc_start: 0.7680 (t80) cc_final: 0.7414 (t80) REVERT: D 108 ASN cc_start: 0.7830 (m-40) cc_final: 0.7566 (m-40) REVERT: D 155 MET cc_start: 0.7941 (mtm) cc_final: 0.7664 (mtt) outliers start: 6 outliers final: 1 residues processed: 107 average time/residue: 0.0699 time to fit residues: 10.2534 Evaluate side-chains 100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103495 restraints weight = 10329.186| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 7961 Z= 0.251 Angle : 0.643 7.728 10797 Z= 0.320 Chirality : 0.047 0.159 1243 Planarity : 0.004 0.038 1341 Dihedral : 7.917 174.634 1060 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.19 % Allowed : 10.63 % Favored : 88.17 % 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: 0.84 (0.27), residues: 979 helix: 1.46 (0.22), residues: 568 sheet: -0.76 (0.64), residues: 63 loop : -0.63 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 249 TYR 0.016 0.002 TYR D 251 PHE 0.013 0.002 PHE A 8 TRP 0.012 0.002 TRP C 108 HIS 0.002 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.25 ( 7961) covalent geometry : angle 0.64311 / 0.32 (10797) hydrogen bonds : bond 0.04845 / 3.34 ( 425) hydrogen bonds : angle 4.22072 / 2.96 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.307 Fit side-chains REVERT: A 184 ASP cc_start: 0.7925 (m-30) cc_final: 0.7436 (m-30) REVERT: A 266 ASP cc_start: 0.7046 (t0) cc_final: 0.6391 (m-30) REVERT: A 268 ASP cc_start: 0.7124 (p0) cc_final: 0.6808 (p0) REVERT: C 129 TRP cc_start: 0.7960 (m-10) cc_final: 0.7572 (m-10) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.0817 time to fit residues: 12.6433 Evaluate side-chains 104 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106959 restraints weight = 10209.328| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.06 r_work: 0.3111 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7961 Z= 0.123 Angle : 0.542 6.440 10797 Z= 0.268 Chirality : 0.042 0.142 1243 Planarity : 0.003 0.038 1341 Dihedral : 7.371 162.263 1060 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.50 % 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: 1.18 (0.27), residues: 979 helix: 1.78 (0.22), residues: 561 sheet: -0.77 (0.62), residues: 68 loop : -0.48 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.023 0.001 TYR D 44 PHE 0.011 0.001 PHE A 246 TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 7961) covalent geometry : angle 0.54190 / 0.27 (10797) hydrogen bonds : bond 0.03847 / 2.66 ( 425) hydrogen bonds : angle 4.01672 / 2.83 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.295 Fit side-chains REVERT: A 184 ASP cc_start: 0.7961 (m-30) cc_final: 0.7447 (m-30) REVERT: A 266 ASP cc_start: 0.6934 (t0) cc_final: 0.6288 (m-30) REVERT: C 129 TRP cc_start: 0.7817 (m-10) cc_final: 0.7473 (m-10) REVERT: D 108 ASN cc_start: 0.7712 (m-40) cc_final: 0.7453 (m-40) outliers start: 9 outliers final: 2 residues processed: 109 average time/residue: 0.0784 time to fit residues: 11.7075 Evaluate side-chains 97 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106457 restraints weight = 10207.548| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.05 r_work: 0.3103 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7961 Z= 0.142 Angle : 0.559 6.941 10797 Z= 0.274 Chirality : 0.043 0.145 1243 Planarity : 0.004 0.038 1341 Dihedral : 6.808 142.475 1060 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 12.90 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 979 helix: 1.87 (0.22), residues: 558 sheet: -0.77 (0.62), residues: 68 loop : -0.48 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.013 0.001 TYR D 251 PHE 0.011 0.001 PHE D 149 TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 7961) covalent geometry : angle 0.55926 / 0.27 (10797) hydrogen bonds : bond 0.03925 / 2.71 ( 425) hydrogen bonds : angle 3.99484 / 2.82 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.281 Fit side-chains REVERT: A 184 ASP cc_start: 0.7947 (m-30) cc_final: 0.7459 (m-30) REVERT: A 266 ASP cc_start: 0.6903 (t0) cc_final: 0.6297 (m-30) REVERT: C 129 TRP cc_start: 0.7796 (m-10) cc_final: 0.7444 (m-10) REVERT: D 108 ASN cc_start: 0.7768 (m-40) cc_final: 0.7492 (m-40) outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.0728 time to fit residues: 10.7620 Evaluate side-chains 101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106604 restraints weight = 10223.088| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.07 r_work: 0.3103 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7961 Z= 0.145 Angle : 0.567 7.030 10797 Z= 0.276 Chirality : 0.043 0.145 1243 Planarity : 0.004 0.038 1341 Dihedral : 6.284 120.067 1060 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 13.38 % Favored : 85.54 % 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: 1.24 (0.27), residues: 979 helix: 1.86 (0.22), residues: 558 sheet: -0.84 (0.62), residues: 68 loop : -0.47 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.023 0.002 TYR D 44 PHE 0.018 0.001 PHE B 252 TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7961) covalent geometry : angle 0.56653 / 0.28 (10797) hydrogen bonds : bond 0.03929 / 2.72 ( 425) hydrogen bonds : angle 4.00121 / 2.83 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.264 Fit side-chains REVERT: A 25 ASP cc_start: 0.7891 (m-30) cc_final: 0.7430 (t0) REVERT: A 184 ASP cc_start: 0.7949 (m-30) cc_final: 0.7461 (m-30) REVERT: A 266 ASP cc_start: 0.6933 (t0) cc_final: 0.6364 (m-30) REVERT: C 129 TRP cc_start: 0.7789 (m-10) cc_final: 0.7437 (m-10) REVERT: D 108 ASN cc_start: 0.7739 (m-40) cc_final: 0.7448 (m-40) outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.0840 time to fit residues: 12.9043 Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108339 restraints weight = 10218.942| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.06 r_work: 0.3136 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7961 Z= 0.113 Angle : 0.545 7.585 10797 Z= 0.265 Chirality : 0.042 0.141 1243 Planarity : 0.003 0.038 1341 Dihedral : 5.742 100.375 1060 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 13.86 % Favored : 84.95 % 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: 1.42 (0.27), residues: 979 helix: 2.01 (0.22), residues: 561 sheet: -0.82 (0.63), residues: 68 loop : -0.42 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.011 0.001 TYR D 251 PHE 0.009 0.001 PHE D 149 TRP 0.012 0.001 TRP B 128 HIS 0.003 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7961) covalent geometry : angle 0.54466 / 0.26 (10797) hydrogen bonds : bond 0.03600 / 2.49 ( 425) hydrogen bonds : angle 3.92294 / 2.78 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.179 Fit side-chains REVERT: A 25 ASP cc_start: 0.7844 (m-30) cc_final: 0.7402 (t0) REVERT: A 184 ASP cc_start: 0.7884 (m-30) cc_final: 0.7391 (m-30) REVERT: A 266 ASP cc_start: 0.6578 (t0) cc_final: 0.6114 (m-30) REVERT: C 129 TRP cc_start: 0.7641 (m-10) cc_final: 0.7330 (m-10) REVERT: D 155 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7531 (mtt) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.0727 time to fit residues: 10.9163 Evaluate side-chains 109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106873 restraints weight = 10176.447| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.05 r_work: 0.3111 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7961 Z= 0.153 Angle : 0.578 8.699 10797 Z= 0.281 Chirality : 0.043 0.145 1243 Planarity : 0.004 0.038 1341 Dihedral : 5.611 90.141 1060 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 13.86 % Favored : 85.07 % 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: 1.28 (0.27), residues: 979 helix: 1.90 (0.22), residues: 558 sheet: -0.88 (0.62), residues: 68 loop : -0.46 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.013 0.001 TYR D 111 PHE 0.012 0.001 PHE A 246 TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 ( 7961) covalent geometry : angle 0.57781 / 0.28 (10797) hydrogen bonds : bond 0.03949 / 2.73 ( 425) hydrogen bonds : angle 4.00285 / 2.83 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.268 Fit side-chains REVERT: A 25 ASP cc_start: 0.7871 (m-30) cc_final: 0.7440 (t0) REVERT: A 184 ASP cc_start: 0.7850 (m-30) cc_final: 0.7362 (m-30) REVERT: A 266 ASP cc_start: 0.6739 (t0) cc_final: 0.6284 (m-30) REVERT: C 129 TRP cc_start: 0.7708 (m-10) cc_final: 0.7358 (m-10) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.0722 time to fit residues: 10.8733 Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109611 restraints weight = 10169.431| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.07 r_work: 0.3148 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7961 Z= 0.106 Angle : 0.550 9.606 10797 Z= 0.267 Chirality : 0.042 0.147 1243 Planarity : 0.003 0.038 1341 Dihedral : 5.239 75.522 1060 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 14.10 % Favored : 85.07 % 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: 1.43 (0.27), residues: 979 helix: 2.03 (0.22), residues: 560 sheet: -0.84 (0.63), residues: 68 loop : -0.43 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.011 0.001 TYR D 111 PHE 0.010 0.001 PHE D 149 TRP 0.013 0.001 TRP B 128 HIS 0.003 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7961) covalent geometry : angle 0.55010 / 0.27 (10797) hydrogen bonds : bond 0.03506 / 2.42 ( 425) hydrogen bonds : angle 3.91167 / 2.78 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.52 seconds wall clock time: 28 minutes 56.16 seconds (1736.16 seconds total)