Starting phenix.real_space_refine on Thu Jul 2 08:28:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmq_16121/07_2026/8bmq_16121.map" } resolution = 3.6 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= 0.010 sd= 0.098 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 6 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5044 2.51 5 N 1283 2.21 5 O 1414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 7784 Number of models: 1 Model: "" Number of chains: 6 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: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2162 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7784 At special positions: 0 Unit cell: (79.716, 83.804, 128.772, 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 6 15.00 Mg 1 11.99 O 1414 8.00 N 1283 7.00 C 5044 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: 0.55 Conformation dependent library (CDL) restraints added in 356.0 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 61.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.793A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 85 removed outlier: 4.215A pdb=" N GLU A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.904A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.217A 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 205 through 210 removed outlier: 3.763A pdb=" N GLY A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.822A pdb=" N PHE A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.912A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.883A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.509A pdb=" N LEU B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.938A pdb=" N ASP B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.800A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.119A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.959A pdb=" N PHE B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.724A pdb=" N LEU B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.798A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.900A pdb=" N LEU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 removed outlier: 3.616A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) 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 54 removed outlier: 3.974A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 4.406A pdb=" N ALA C 62 " --> pdb=" O TRP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 removed outlier: 3.894A pdb=" N THR C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY C 92 " --> pdb=" O THR C 88 " (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 125 through 135 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.538A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 152 through 172 removed outlier: 4.720A pdb=" N VAL C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.593A 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 37 removed outlier: 3.923A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 3.554A pdb=" N GLY D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.217A 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 removed outlier: 3.793A pdb=" N ARG D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) 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 185 removed outlier: 4.019A pdb=" N ILE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 191 through 199 removed outlier: 4.136A pdb=" N LYS D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 226 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 245 through 262 removed outlier: 3.856A pdb=" N VAL D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR D 256 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.301A pdb=" N ILE A 165 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 200 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 167 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 30 removed outlier: 5.238A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.008A pdb=" N ALA B 90 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 36 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 225 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.298A 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 35 421 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.73 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: 2451 1.34 - 1.46: 1198 1.46 - 1.57: 4220 1.57 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 7949 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP B 301 " pdb=" PB ANP B 301 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O5' ANP A 301 " pdb=" PA ANP A 301 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 7944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10729 3.84 - 7.68: 42 7.68 - 11.52: 8 11.52 - 15.36: 0 15.36 - 19.20: 2 Bond angle restraints: 10781 Sorted by residual: angle pdb=" PB ANP A 301 " pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP B 301 " pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 126.95 107.82 19.13 3.00e+00 1.11e-01 4.06e+01 angle pdb=" O1B ANP B 301 " pdb=" PB ANP B 301 " pdb=" O2B ANP B 301 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C LEU A 174 " pdb=" N ASP A 175 " pdb=" CA ASP A 175 " ideal model delta sigma weight residual 120.65 125.64 -4.99 1.36e+00 5.41e-01 1.35e+01 angle pdb=" O1B ANP A 301 " pdb=" PB ANP A 301 " pdb=" O2B ANP A 301 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 10776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4249 17.69 - 35.39: 371 35.39 - 53.08: 58 53.08 - 70.78: 16 70.78 - 88.47: 5 Dihedral angle restraints: 4699 sinusoidal: 1875 harmonic: 2824 Sorted by residual: dihedral pdb=" CA SER A 103 " pdb=" C SER A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " pdb=" OD1 ASP A 211 " ideal model delta sinusoidal sigma weight residual -30.00 -85.09 55.09 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA THR B 197 " pdb=" C THR B 197 " pdb=" N VAL B 198 " pdb=" CA VAL B 198 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1027 0.056 - 0.113: 190 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C3' ANP B 301 " pdb=" C2' ANP B 301 " pdb=" C4' ANP B 301 " pdb=" O3' ANP B 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' ANP A 301 " pdb=" C2' ANP A 301 " pdb=" C4' ANP A 301 " pdb=" O3' ANP A 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1240 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 47 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C GLY C 47 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY C 47 " 0.011 2.00e-02 2.50e+03 pdb=" N SER C 48 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 93 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 198 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL B 198 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 198 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 199 " -0.009 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 545 2.73 - 3.27: 7949 3.27 - 3.82: 12315 3.82 - 4.36: 14288 4.36 - 4.90: 25457 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" O1B ANP B 301 " pdb=" O2G ANP B 301 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASN D 40 " pdb=" N TRP D 41 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP B 170 " pdb="MG MG B 302 " model vdw 2.251 2.170 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.253 3.040 ... (remaining 60549 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.110 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.006 0.146 7949 Z= 0.271 Angle : 0.756 19.200 10781 Z= 0.355 Chirality : 0.046 0.282 1243 Planarity : 0.004 0.041 1336 Dihedral : 13.789 88.472 2879 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 975 helix: 0.76 (0.23), residues: 547 sheet: -0.74 (0.60), residues: 70 loop : -1.07 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 263 TYR 0.027 0.002 TYR D 54 PHE 0.020 0.002 PHE D 86 TRP 0.010 0.001 TRP C 58 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.27 ( 7949) covalent geometry : angle 0.75615 / 0.35 (10781) hydrogen bonds : bond 0.14996 / 9.88 ( 421) hydrogen bonds : angle 5.58643 / 3.91 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.272 Fit side-chains REVERT: B 82 ASP cc_start: 0.5800 (m-30) cc_final: 0.5558 (m-30) REVERT: C 157 MET cc_start: 0.7164 (mtm) cc_final: 0.6944 (mtp) REVERT: D 126 MET cc_start: 0.8272 (tpp) cc_final: 0.8029 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0664 time to fit residues: 10.5852 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147882 restraints weight = 9497.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147867 restraints weight = 8754.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148659 restraints weight = 7945.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148989 restraints weight = 7051.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149022 restraints weight = 6544.095| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7949 Z= 0.130 Angle : 0.527 10.018 10781 Z= 0.269 Chirality : 0.042 0.200 1243 Planarity : 0.004 0.045 1336 Dihedral : 5.480 53.407 1051 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.48 % Allowed : 8.98 % Favored : 90.54 % 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: 0.40 (0.28), residues: 975 helix: 1.17 (0.23), residues: 550 sheet: -0.60 (0.62), residues: 70 loop : -0.93 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.017 0.002 TYR D 54 PHE 0.010 0.001 PHE B 188 TRP 0.014 0.001 TRP A 276 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7949) covalent geometry : angle 0.52696 / 0.27 (10781) hydrogen bonds : bond 0.04034 / 2.68 ( 421) hydrogen bonds : angle 4.28572 / 3.03 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.183 Fit side-chains REVERT: D 126 MET cc_start: 0.8397 (tpp) cc_final: 0.8147 (tpp) outliers start: 4 outliers final: 4 residues processed: 98 average time/residue: 0.0592 time to fit residues: 8.6215 Evaluate side-chains 98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118601 restraints weight = 10698.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121999 restraints weight = 7001.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124297 restraints weight = 5262.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125831 restraints weight = 4333.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126925 restraints weight = 3784.305| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7949 Z= 0.227 Angle : 0.608 10.520 10781 Z= 0.309 Chirality : 0.045 0.178 1243 Planarity : 0.004 0.051 1336 Dihedral : 5.705 56.995 1051 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.44 % Allowed : 11.98 % Favored : 86.59 % 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: 0.14 (0.27), residues: 975 helix: 0.95 (0.23), residues: 550 sheet: -0.73 (0.63), residues: 70 loop : -1.02 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 225 TYR 0.024 0.002 TYR D 54 PHE 0.016 0.002 PHE B 35 TRP 0.018 0.001 TRP A 276 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 ( 7949) covalent geometry : angle 0.60814 / 0.31 (10781) hydrogen bonds : bond 0.04189 / 2.78 ( 421) hydrogen bonds : angle 4.37125 / 3.10 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 126 MET cc_start: 0.8470 (tpp) cc_final: 0.8060 (tpp) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.0683 time to fit residues: 10.7483 Evaluate side-chains 104 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126717 restraints weight = 10825.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128786 restraints weight = 8315.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129635 restraints weight = 6543.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130287 restraints weight = 5709.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130382 restraints weight = 5292.261| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7949 Z= 0.153 Angle : 0.532 10.056 10781 Z= 0.271 Chirality : 0.043 0.171 1243 Planarity : 0.004 0.054 1336 Dihedral : 5.609 57.153 1051 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.68 % Allowed : 14.01 % Favored : 84.31 % 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: 0.28 (0.28), residues: 975 helix: 1.08 (0.23), residues: 558 sheet: -0.74 (0.62), residues: 70 loop : -1.01 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.019 0.002 TYR D 17 PHE 0.015 0.001 PHE D 86 TRP 0.019 0.001 TRP A 276 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 ( 7949) covalent geometry : angle 0.53244 / 0.27 (10781) hydrogen bonds : bond 0.03593 / 2.40 ( 421) hydrogen bonds : angle 4.14423 / 2.94 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.250 Fit side-chains REVERT: C 100 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7136 (pp) REVERT: D 126 MET cc_start: 0.8479 (tpp) cc_final: 0.8248 (tpp) REVERT: D 190 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: D 196 ARG cc_start: 0.6510 (ttp-170) cc_final: 0.6022 (mtt-85) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.0700 time to fit residues: 10.7485 Evaluate side-chains 107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.0370 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147996 restraints weight = 9410.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148123 restraints weight = 8343.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148751 restraints weight = 7674.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149225 restraints weight = 6937.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149451 restraints weight = 6390.003| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7949 Z= 0.112 Angle : 0.494 9.353 10781 Z= 0.251 Chirality : 0.041 0.165 1243 Planarity : 0.004 0.058 1336 Dihedral : 5.438 57.491 1051 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.44 % Allowed : 14.85 % Favored : 83.71 % 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: 0.60 (0.28), residues: 975 helix: 1.35 (0.23), residues: 557 sheet: -0.58 (0.62), residues: 70 loop : -0.92 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.017 0.001 TYR D 17 PHE 0.014 0.001 PHE D 86 TRP 0.021 0.001 TRP A 276 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7949) covalent geometry : angle 0.49446 / 0.25 (10781) hydrogen bonds : bond 0.03142 / 2.11 ( 421) hydrogen bonds : angle 3.94814 / 2.79 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.170 Fit side-chains REVERT: B 66 ILE cc_start: 0.8481 (tp) cc_final: 0.8116 (tp) REVERT: C 100 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7197 (pp) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.0566 time to fit residues: 8.6109 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 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 = 0.3930 r_free = 0.3930 target = 0.164276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145586 restraints weight = 9466.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145616 restraints weight = 8710.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145992 restraints weight = 8339.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146331 restraints weight = 7336.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146520 restraints weight = 7077.739| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7949 Z= 0.150 Angle : 0.529 9.939 10781 Z= 0.267 Chirality : 0.042 0.157 1243 Planarity : 0.004 0.060 1336 Dihedral : 5.474 58.728 1051 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.16 % Allowed : 15.09 % Favored : 82.75 % 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: 0.55 (0.28), residues: 975 helix: 1.34 (0.23), residues: 555 sheet: -0.66 (0.62), residues: 70 loop : -0.97 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.020 0.002 TYR B 12 PHE 0.017 0.001 PHE D 86 TRP 0.024 0.001 TRP A 276 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7949) covalent geometry : angle 0.52888 / 0.27 (10781) hydrogen bonds : bond 0.03413 / 2.28 ( 421) hydrogen bonds : angle 4.03294 / 2.85 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.228 Fit side-chains REVERT: B 66 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8156 (tp) REVERT: C 100 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7235 (pp) REVERT: D 196 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.6451 (mtt-85) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.0616 time to fit residues: 9.8301 Evaluate side-chains 111 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 257 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.148268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117925 restraints weight = 10728.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121335 restraints weight = 7013.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123581 restraints weight = 5254.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125123 restraints weight = 4336.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125997 restraints weight = 3781.887| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7949 Z= 0.210 Angle : 0.601 10.413 10781 Z= 0.302 Chirality : 0.045 0.158 1243 Planarity : 0.004 0.060 1336 Dihedral : 5.677 59.484 1051 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.51 % Allowed : 15.33 % Favored : 82.16 % 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: 0.27 (0.27), residues: 975 helix: 1.14 (0.23), residues: 550 sheet: -0.88 (0.61), residues: 70 loop : -1.08 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 184 TYR 0.023 0.002 TYR D 17 PHE 0.020 0.002 PHE D 86 TRP 0.027 0.002 TRP A 276 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 ( 7949) covalent geometry : angle 0.60129 / 0.30 (10781) hydrogen bonds : bond 0.03899 / 2.59 ( 421) hydrogen bonds : angle 4.24362 / 3.00 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 100 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7130 (pp) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.0682 time to fit residues: 11.1296 Evaluate side-chains 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 257 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.166686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147862 restraints weight = 9452.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148271 restraints weight = 8446.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148532 restraints weight = 7853.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148926 restraints weight = 7584.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149116 restraints weight = 6774.535| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7949 Z= 0.107 Angle : 0.505 9.463 10781 Z= 0.254 Chirality : 0.041 0.154 1243 Planarity : 0.004 0.061 1336 Dihedral : 5.376 58.886 1051 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.68 % Allowed : 16.41 % Favored : 81.92 % 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: 0.67 (0.28), residues: 975 helix: 1.46 (0.23), residues: 556 sheet: -0.64 (0.62), residues: 70 loop : -0.94 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 225 TYR 0.016 0.001 TYR D 17 PHE 0.016 0.001 PHE D 86 TRP 0.015 0.001 TRP A 276 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7949) covalent geometry : angle 0.50463 / 0.25 (10781) hydrogen bonds : bond 0.03051 / 2.06 ( 421) hydrogen bonds : angle 3.93680 / 2.79 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.269 Fit side-chains REVERT: B 66 ILE cc_start: 0.8476 (tp) cc_final: 0.8121 (tp) REVERT: C 100 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7245 (pp) REVERT: C 157 MET cc_start: 0.7083 (mtp) cc_final: 0.6859 (mtp) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.0635 time to fit residues: 9.8334 Evaluate side-chains 107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147571 restraints weight = 9498.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147721 restraints weight = 8777.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148297 restraints weight = 7822.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148705 restraints weight = 7000.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149268 restraints weight = 6587.485| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7949 Z= 0.119 Angle : 0.513 9.175 10781 Z= 0.260 Chirality : 0.041 0.157 1243 Planarity : 0.004 0.060 1336 Dihedral : 5.275 59.292 1051 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.68 % Allowed : 16.53 % Favored : 81.80 % 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: 0.70 (0.28), residues: 975 helix: 1.44 (0.23), residues: 556 sheet: -0.58 (0.61), residues: 70 loop : -0.87 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.013 0.001 TYR D 54 PHE 0.018 0.001 PHE D 86 TRP 0.029 0.001 TRP A 276 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7949) covalent geometry : angle 0.51346 / 0.26 (10781) hydrogen bonds : bond 0.03157 / 2.12 ( 421) hydrogen bonds : angle 3.96293 / 2.82 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.269 Fit side-chains REVERT: B 66 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8110 (tp) REVERT: C 100 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7258 (pp) REVERT: C 157 MET cc_start: 0.7026 (mtp) cc_final: 0.6823 (mtp) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.0631 time to fit residues: 9.7335 Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.7980 chunk 94 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147260 restraints weight = 9458.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146708 restraints weight = 7944.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146782 restraints weight = 7442.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147080 restraints weight = 7352.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147196 restraints weight = 6907.399| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7949 Z= 0.146 Angle : 0.537 9.935 10781 Z= 0.271 Chirality : 0.042 0.155 1243 Planarity : 0.004 0.060 1336 Dihedral : 5.290 59.790 1051 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.04 % Allowed : 16.05 % Favored : 81.92 % 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: 0.61 (0.28), residues: 975 helix: 1.37 (0.23), residues: 556 sheet: -0.69 (0.61), residues: 70 loop : -0.88 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.018 0.001 TYR D 17 PHE 0.019 0.001 PHE D 86 TRP 0.028 0.001 TRP A 276 HIS 0.002 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 7949) covalent geometry : angle 0.53660 / 0.27 (10781) hydrogen bonds : bond 0.03376 / 2.25 ( 421) hydrogen bonds : angle 4.04230 / 2.88 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.265 Fit side-chains REVERT: B 66 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7921 (tp) REVERT: C 100 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7268 (pp) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.0635 time to fit residues: 9.9910 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149430 restraints weight = 9382.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149613 restraints weight = 8363.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150069 restraints weight = 7710.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150391 restraints weight = 6854.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150561 restraints weight = 6605.402| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7949 Z= 0.106 Angle : 0.503 9.015 10781 Z= 0.255 Chirality : 0.041 0.157 1243 Planarity : 0.004 0.060 1336 Dihedral : 5.118 58.712 1051 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.80 % Allowed : 16.89 % Favored : 81.32 % 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: 0.79 (0.28), residues: 975 helix: 1.52 (0.23), residues: 554 sheet: -0.53 (0.62), residues: 70 loop : -0.84 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.013 0.001 TYR D 251 PHE 0.017 0.001 PHE D 86 TRP 0.030 0.001 TRP A 276 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 7949) covalent geometry : angle 0.50252 / 0.26 (10781) hydrogen bonds : bond 0.03000 / 2.01 ( 421) hydrogen bonds : angle 3.92015 / 2.79 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 962.00 seconds wall clock time: 17 minutes 18.90 seconds (1038.90 seconds total)