Starting phenix.real_space_refine on Fri Aug 22 14:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6q_35203/08_2025/8i6q_35203.map" } resolution = 4.23 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= -0.001 sd= 0.029 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: 3 Type Number sf(0) Gaussians C 2354 2.51 5 N 810 2.21 5 O 811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 884 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 176} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 724 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'TYR:plan': 5, 'GLU:plan': 7, 'HIS:plan': 4, 'ARG:plan': 12, 'ASP:plan': 5, 'PHE:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 276 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1090 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'ARG:plan': 22, 'PHE:plan': 6, 'GLU:plan': 13, 'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 904 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'PHE:plan': 8, 'TYR:plan': 5, 'GLU:plan': 8, 'HIS:plan': 4, 'ARG:plan': 13, 'ASP:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 285 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1097 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 651 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'ARG:plan': 22, 'PHE:plan': 6, 'GLU:plan': 13, 'GLN:plan1': 12, 'ASN:plan1': 6, 'HIS:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 334 Time building chain proxies: 1.44, per 1000 atoms: 0.36 Number of scatterers: 3975 At special positions: 0 Unit cell: (81.51, 76.362, 120.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 811 8.00 N 810 7.00 C 2354 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: 0.40 Conformation dependent library (CDL) restraints added in 246.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 64.3% alpha, 3.7% 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 35 through 54 Processing helix chain 'A' and resid 55 through 78 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.509A pdb=" N TRP A 193 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 196 No H-bonds generated for 'chain 'A' and resid 195 through 196' Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.754A pdb=" N LEU A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 233 removed outlier: 4.248A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 247 through 283 Proline residue: A 254 - end of helix removed outlier: 3.649A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 333 removed outlier: 4.128A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 72 through 79 removed outlier: 4.011A pdb=" N PHE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.514A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 4.231A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 197 through 203 removed outlier: 4.020A pdb=" N ARG B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 57 through 87 Proline residue: C 73 - end of helix removed outlier: 4.532A pdb=" N LEU C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 202 through 233 removed outlier: 4.312A pdb=" N ARG C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 247 through 283 Proline residue: C 254 - end of helix removed outlier: 3.882A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 310 through 330 removed outlier: 5.363A pdb=" N ALA C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 322 " --> pdb=" O TRP C 318 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 72 through 81 removed outlier: 4.431A pdb=" N PHE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 110 through 125 removed outlier: 4.097A pdb=" N ARG D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 139 through 153 Processing helix chain 'D' and resid 169 through 186 Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.518A pdb=" N MET D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25 removed outlier: 5.130A pdb=" N PHE B 4 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 60 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN B 6 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.502A pdb=" N LEU B 191 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 31 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER B 194 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 33 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 208 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 9 through 11 removed outlier: 5.823A pdb=" N LYS D 9 " --> pdb=" O GLY D 17 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1032 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: 0.58 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 810 1.29 - 1.36: 802 1.36 - 1.42: 7 1.42 - 1.48: 810 1.48 - 1.55: 1539 Bond restraints: 3968 Sorted by residual: bond pdb=" N GLN B 142 " pdb=" CA GLN B 142 " ideal model delta sigma weight residual 1.459 1.433 0.026 1.21e-02 6.83e+03 4.53e+00 bond pdb=" CA GLN B 155 " pdb=" C GLN B 155 " ideal model delta sigma weight residual 1.531 1.517 0.014 7.40e-03 1.83e+04 3.68e+00 bond pdb=" CA GLY C 249 " pdb=" C GLY C 249 " ideal model delta sigma weight residual 1.516 1.500 0.016 1.12e-02 7.97e+03 2.12e+00 bond pdb=" C GLU D 163 " pdb=" N PRO D 164 " ideal model delta sigma weight residual 1.334 1.301 0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C GLN D 155 " pdb=" O GLN D 155 " ideal model delta sigma weight residual 1.235 1.228 0.006 4.70e-03 4.53e+04 1.91e+00 ... (remaining 3963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5178 1.35 - 2.71: 266 2.71 - 4.06: 36 4.06 - 5.41: 9 5.41 - 6.76: 4 Bond angle restraints: 5493 Sorted by residual: angle pdb=" C THR B 55 " pdb=" CA THR B 55 " pdb=" CB THR B 55 " ideal model delta sigma weight residual 116.54 110.07 6.47 1.15e+00 7.56e-01 3.16e+01 angle pdb=" N GLY B 57 " pdb=" CA GLY B 57 " pdb=" C GLY B 57 " ideal model delta sigma weight residual 111.85 116.48 -4.63 1.06e+00 8.90e-01 1.91e+01 angle pdb=" CA TYR D 11 " pdb=" CB TYR D 11 " pdb=" CG TYR D 11 " ideal model delta sigma weight residual 113.90 119.62 -5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C GLY C 245 " pdb=" N GLY C 246 " pdb=" CA GLY C 246 " ideal model delta sigma weight residual 121.32 116.43 4.89 1.58e+00 4.01e-01 9.56e+00 angle pdb=" N GLU B 132 " pdb=" CA GLU B 132 " pdb=" C GLU B 132 " ideal model delta sigma weight residual 111.36 114.66 -3.30 1.09e+00 8.42e-01 9.15e+00 ... (remaining 5488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.91: 2043 5.91 - 11.82: 172 11.82 - 17.73: 35 17.73 - 23.64: 8 23.64 - 29.55: 3 Dihedral angle restraints: 2261 sinusoidal: 2 harmonic: 2259 Sorted by residual: dihedral pdb=" CA ARG D 10 " pdb=" C ARG D 10 " pdb=" N TYR D 11 " pdb=" CA TYR D 11 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ARG D 185 " pdb=" C ARG D 185 " pdb=" N LEU D 186 " pdb=" CA LEU D 186 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ARG B 185 " pdb=" C ARG B 185 " pdb=" N LEU B 186 " pdb=" CA LEU B 186 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 2258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 437 0.026 - 0.053: 143 0.053 - 0.079: 102 0.079 - 0.106: 39 0.106 - 0.132: 7 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA PRO D 170 " pdb=" N PRO D 170 " pdb=" C PRO D 170 " pdb=" CB PRO D 170 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL C 301 " pdb=" N VAL C 301 " pdb=" C VAL C 301 " pdb=" CB VAL C 301 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 725 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 11 " 0.016 2.00e-02 2.50e+03 1.30e-02 3.39e+00 pdb=" CG TYR D 11 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 11 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 11 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 11 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 11 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 21 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C VAL B 21 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL B 21 " 0.011 2.00e-02 2.50e+03 pdb=" N SER B 22 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 122 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LEU D 122 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU D 122 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU D 123 " 0.009 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 44 2.60 - 3.18: 4580 3.18 - 3.75: 6332 3.75 - 4.33: 7457 4.33 - 4.90: 10306 Nonbonded interactions: 28719 Sorted by model distance: nonbonded pdb=" O HIS C 55 " pdb=" N SER C 59 " model vdw 2.031 3.120 nonbonded pdb=" O ILE D 2 " pdb=" N VAL D 25 " model vdw 2.230 3.120 nonbonded pdb=" O LEU A 70 " pdb=" N MET A 74 " model vdw 2.261 3.120 nonbonded pdb=" N HIS B 19 " pdb=" O GLY B 213 " model vdw 2.318 3.120 nonbonded pdb=" N GLN D 6 " pdb=" O VAL D 21 " model vdw 2.332 3.120 ... (remaining 28714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 283 or resid 298 through 332)) selection = (chain 'C' and (resid 35 through 83 or resid 190 through 283 or resid 298 throug \ h 332)) } ncs_group { reference = chain 'B' selection = (chain 'D' and ((resid 1 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 through 222)) } 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: 2.690 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.510 Find NCS groups from input model: 0.070 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.005 0.033 3968 Z= 0.388 Angle : 0.734 6.764 5493 Z= 0.518 Chirality : 0.040 0.132 728 Planarity : 0.004 0.017 803 Dihedral : 6.123 29.547 805 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.28), residues: 794 helix: -0.21 (0.23), residues: 449 sheet: -2.80 (0.88), residues: 34 loop : -2.13 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.004 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 3968) covalent geometry : angle 0.73364 ( 5493) hydrogen bonds : bond 0.24031 ( 352) hydrogen bonds : angle 7.51597 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.145 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0173 time to fit residues: 0.7423 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 90.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 74 optimal weight: 0.8980 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.034476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027193 restraints weight = 65290.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027334 restraints weight = 59102.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.027438 restraints weight = 54712.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.027540 restraints weight = 50884.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.027612 restraints weight = 48923.891| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3968 Z= 0.259 Angle : 0.547 7.652 5493 Z= 0.357 Chirality : 0.040 0.128 728 Planarity : 0.003 0.013 803 Dihedral : 5.442 26.417 803 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.29), residues: 794 helix: 0.26 (0.22), residues: 489 sheet: -2.79 (0.81), residues: 46 loop : -2.18 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3968) covalent geometry : angle 0.54651 ( 5493) hydrogen bonds : bond 0.06080 ( 352) hydrogen bonds : angle 5.87135 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0119 time to fit residues: 0.5089 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 50.0000 chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.033019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.025010 restraints weight = 72611.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.025010 restraints weight = 70300.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.025010 restraints weight = 70300.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.025010 restraints weight = 70300.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.025010 restraints weight = 70300.966| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3968 Z= 0.180 Angle : 0.446 6.173 5493 Z= 0.287 Chirality : 0.039 0.132 728 Planarity : 0.002 0.009 803 Dihedral : 4.625 24.546 803 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 100.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.30), residues: 794 helix: 1.20 (0.23), residues: 491 sheet: -2.70 (0.91), residues: 34 loop : -2.16 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3968) covalent geometry : angle 0.44577 ( 5493) hydrogen bonds : bond 0.04256 ( 352) hydrogen bonds : angle 4.95014 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0180 time to fit residues: 0.7751 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.034806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.027460 restraints weight = 64049.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027589 restraints weight = 58564.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027662 restraints weight = 54975.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027776 restraints weight = 51771.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 13)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027821 restraints weight = 49306.101| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3968 Z= 0.216 Angle : 0.477 6.885 5493 Z= 0.310 Chirality : 0.039 0.130 728 Planarity : 0.002 0.010 803 Dihedral : 4.621 24.675 803 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.30), residues: 794 helix: 1.28 (0.23), residues: 490 sheet: -2.71 (0.93), residues: 34 loop : -2.21 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.003 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3968) covalent geometry : angle 0.47653 ( 5493) hydrogen bonds : bond 0.04326 ( 352) hydrogen bonds : angle 4.85692 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0167 time to fit residues: 0.7199 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.034381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.028298 restraints weight = 84066.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.028409 restraints weight = 75427.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.028510 restraints weight = 69047.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.028588 restraints weight = 64379.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.028667 restraints weight = 60248.228| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3968 Z= 0.127 Angle : 0.390 5.493 5493 Z= 0.247 Chirality : 0.039 0.126 728 Planarity : 0.002 0.008 803 Dihedral : 4.057 23.431 803 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.32), residues: 794 helix: 2.16 (0.24), residues: 491 sheet: -2.12 (0.88), residues: 43 loop : -2.13 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 3968) covalent geometry : angle 0.39013 ( 5493) hydrogen bonds : bond 0.03379 ( 352) hydrogen bonds : angle 4.18735 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0196 time to fit residues: 0.8579 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 61 optimal weight: 40.0000 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 110.0000 chunk 43 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 50.0000 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.027608 restraints weight = 80015.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.027724 restraints weight = 71794.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.027822 restraints weight = 65635.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.027852 restraints weight = 60928.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.027852 restraints weight = 59612.126| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3968 Z= 0.170 Angle : 0.426 5.811 5493 Z= 0.274 Chirality : 0.039 0.126 728 Planarity : 0.002 0.008 803 Dihedral : 4.133 23.384 803 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.31), residues: 794 helix: 2.15 (0.23), residues: 493 sheet: -2.26 (0.86), residues: 43 loop : -2.12 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3968) covalent geometry : angle 0.42590 ( 5493) hydrogen bonds : bond 0.03618 ( 352) hydrogen bonds : angle 4.22798 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0180 time to fit residues: 0.7832 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027720 restraints weight = 64346.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027861 restraints weight = 58784.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027960 restraints weight = 54760.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.028037 restraints weight = 51886.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.028037 restraints weight = 49366.269| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 3968 Z= 0.093 Angle : 0.363 4.971 5493 Z= 0.227 Chirality : 0.039 0.121 728 Planarity : 0.002 0.006 803 Dihedral : 3.811 22.160 803 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.32), residues: 794 helix: 2.73 (0.24), residues: 494 sheet: -2.24 (0.76), residues: 52 loop : -1.94 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00122 ( 3968) covalent geometry : angle 0.36345 ( 5493) hydrogen bonds : bond 0.02957 ( 352) hydrogen bonds : angle 3.79501 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0180 time to fit residues: 0.7991 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 74 optimal weight: 0.0770 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 3.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.035009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027619 restraints weight = 64368.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027768 restraints weight = 58974.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027853 restraints weight = 54754.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027950 restraints weight = 51541.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.028001 restraints weight = 49561.455| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3968 Z= 0.126 Angle : 0.382 5.086 5493 Z= 0.243 Chirality : 0.039 0.124 728 Planarity : 0.002 0.007 803 Dihedral : 3.769 21.957 803 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.32), residues: 794 helix: 2.87 (0.23), residues: 493 sheet: -2.18 (0.84), residues: 43 loop : -1.93 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 3968) covalent geometry : angle 0.38224 ( 5493) hydrogen bonds : bond 0.03069 ( 352) hydrogen bonds : angle 3.74733 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.145 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0179 time to fit residues: 0.7911 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 5 optimal weight: 110.0000 chunk 28 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.033661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025549 restraints weight = 66799.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025549 restraints weight = 65057.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025549 restraints weight = 65057.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025549 restraints weight = 65050.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025549 restraints weight = 65044.057| |-----------------------------------------------------------------------------| r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3968 Z= 0.176 Angle : 0.419 5.347 5493 Z= 0.273 Chirality : 0.039 0.123 728 Planarity : 0.002 0.008 803 Dihedral : 3.921 22.154 803 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.32), residues: 794 helix: 2.70 (0.23), residues: 493 sheet: -2.17 (0.84), residues: 43 loop : -1.97 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3968) covalent geometry : angle 0.41867 ( 5493) hydrogen bonds : bond 0.03432 ( 352) hydrogen bonds : angle 3.95377 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0180 time to fit residues: 0.8354 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.034547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.028342 restraints weight = 81207.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.028448 restraints weight = 73202.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.028560 restraints weight = 67078.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.028644 restraints weight = 62206.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028711 restraints weight = 58356.147| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 3968 Z= 0.086 Angle : 0.355 4.588 5493 Z= 0.221 Chirality : 0.039 0.123 728 Planarity : 0.001 0.007 803 Dihedral : 3.635 21.241 803 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.32), residues: 794 helix: 3.17 (0.23), residues: 493 sheet: -1.84 (0.88), residues: 38 loop : -1.91 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00114 ( 3968) covalent geometry : angle 0.35466 ( 5493) hydrogen bonds : bond 0.02794 ( 352) hydrogen bonds : angle 3.57116 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0187 time to fit residues: 0.8319 Evaluate side-chains 18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 0.0020 chunk 39 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.034878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027548 restraints weight = 64683.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027673 restraints weight = 59093.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.027808 restraints weight = 54238.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.027887 restraints weight = 51322.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.027960 restraints weight = 49524.853| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3968 Z= 0.144 Angle : 0.394 4.900 5493 Z= 0.253 Chirality : 0.039 0.123 728 Planarity : 0.002 0.008 803 Dihedral : 3.724 21.557 803 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.32), residues: 794 helix: 3.07 (0.23), residues: 494 sheet: -1.86 (0.89), residues: 38 loop : -1.89 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR D 11 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 193 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 3968) covalent geometry : angle 0.39383 ( 5493) hydrogen bonds : bond 0.03122 ( 352) hydrogen bonds : angle 3.69435 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 804.67 seconds wall clock time: 14 minutes 23.31 seconds (863.31 seconds total)