Starting phenix.real_space_refine on Sun Jun 8 15:52:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge7_51292/06_2025/9ge7_51292.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 2 5.21 5 S 42 5.16 5 C 6219 2.51 5 N 1725 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9773 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6295 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 760} Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1707 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1707 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} 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} Chain: "C" 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: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9773 At special positions: 0 Unit cell: (139.445, 88.51, 106.88, 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 42 16.00 P 6 15.00 Mg 2 11.99 O 1779 8.00 N 1725 7.00 C 6219 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 55.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 12 through 49 removed outlier: 3.677A pdb=" N GLU A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 4.208A pdb=" N LEU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.520A pdb=" N MET A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.965A pdb=" N ASP A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 233 through 280 removed outlier: 3.863A pdb=" N MET A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 321 Processing helix chain 'A' and resid 334 through 361 removed outlier: 3.735A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 343 " --> pdb=" O TRP A 339 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 378 through 399 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 401 through 430 removed outlier: 3.575A pdb=" N TRP A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 4.050A pdb=" N GLN A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 485 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.521A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 663 through 707 removed outlier: 3.540A pdb=" N GLN A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 707 " --> pdb=" O GLY A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 720 through 758 removed outlier: 3.652A pdb=" N ILE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 794 removed outlier: 3.515A pdb=" N TRP A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Proline residue: A 774 - end of helix removed outlier: 3.509A pdb=" N LYS A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 804 removed outlier: 3.922A pdb=" N ALA A 803 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.410A pdb=" N GLY B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 197 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.260A pdb=" N MET C 77 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 104 through 117 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 119 through 135 Processing helix chain 'C' and resid 148 through 164 removed outlier: 3.637A pdb=" N ARG C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.519A pdb=" N ALA C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 8.702A pdb=" N LEU A 174 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN A 98 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N MET A 176 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS A 100 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 177 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N SER A 125 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU A 128 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 156 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 497 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 492 through 497 current: chain 'A' and resid 533 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 533 through 534 current: chain 'A' and resid 600 through 608 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 16 removed outlier: 6.360A pdb=" N LEU B 12 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 27 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 14 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.467A pdb=" N GLY B 91 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 39 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS B 216 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 23 through 33 removed outlier: 6.308A pdb=" N LYS C 14 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 27 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU C 12 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 29 " --> pdb=" O HIS C 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS C 10 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 31 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL C 9 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SER C 68 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS C 11 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU C 66 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 93 removed outlier: 6.392A pdb=" N GLY C 91 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP C 171 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 93 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU C 168 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 203 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA C 170 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS C 216 " --> pdb=" O GLU C 227 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.00 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: 3270 1.34 - 1.46: 2054 1.46 - 1.58: 4548 1.58 - 1.70: 8 1.70 - 1.82: 76 Bond restraints: 9956 Sorted by residual: bond pdb=" CB MET A 51 " pdb=" CG MET A 51 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB TRP A 481 " pdb=" CG TRP A 481 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.02e+00 bond pdb=" CA VAL A 259 " pdb=" C VAL A 259 " ideal model delta sigma weight residual 1.524 1.511 0.012 1.22e-02 6.72e+03 9.97e-01 bond pdb=" CA PRO B 73 " pdb=" C PRO B 73 " ideal model delta sigma weight residual 1.527 1.517 0.010 1.07e-02 8.73e+03 9.49e-01 bond pdb=" CB TRP A 337 " pdb=" CG TRP A 337 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.88e-01 ... (remaining 9951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 13268 2.04 - 4.07: 215 4.07 - 6.11: 35 6.11 - 8.15: 5 8.15 - 10.19: 3 Bond angle restraints: 13526 Sorted by residual: angle pdb=" CB LYS A 100 " pdb=" CG LYS A 100 " pdb=" CD LYS A 100 " ideal model delta sigma weight residual 111.30 118.71 -7.41 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CA LEU A 426 " pdb=" CB LEU A 426 " pdb=" CG LEU A 426 " ideal model delta sigma weight residual 116.30 126.49 -10.19 3.50e+00 8.16e-02 8.47e+00 angle pdb=" CA GLU A 40 " pdb=" CB GLU A 40 " pdb=" CG GLU A 40 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.38e+00 angle pdb=" CB MET A 432 " pdb=" CG MET A 432 " pdb=" SD MET A 432 " ideal model delta sigma weight residual 112.70 121.22 -8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" CA LYS C 184 " pdb=" CB LYS C 184 " pdb=" CG LYS C 184 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.07e+00 ... (remaining 13521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 5234 16.91 - 33.82: 603 33.82 - 50.73: 138 50.73 - 67.64: 39 67.64 - 84.54: 4 Dihedral angle restraints: 6018 sinusoidal: 2453 harmonic: 3565 Sorted by residual: dihedral pdb=" CA HIS C 89 " pdb=" C HIS C 89 " pdb=" N VAL C 90 " pdb=" CA VAL C 90 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LYS B 88 " pdb=" C LYS B 88 " pdb=" N HIS B 89 " pdb=" CA HIS B 89 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP C 183 " pdb=" CB ASP C 183 " pdb=" CG ASP C 183 " pdb=" OD1 ASP C 183 " ideal model delta sinusoidal sigma weight residual -30.00 -84.50 54.50 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 6015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1036 0.031 - 0.061: 367 0.061 - 0.092: 97 0.092 - 0.122: 60 0.122 - 0.153: 5 Chirality restraints: 1565 Sorted by residual: chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA TRP A 335 " pdb=" N TRP A 335 " pdb=" C TRP A 335 " pdb=" CB TRP A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA PRO A 450 " pdb=" N PRO A 450 " pdb=" C PRO A 450 " pdb=" CB PRO A 450 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1562 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 261 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C VAL A 261 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A 261 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 262 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 259 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C VAL A 259 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 259 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 260 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 257 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ALA A 257 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA A 257 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 258 " -0.012 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 78 2.43 - 3.05: 6779 3.05 - 3.67: 15532 3.67 - 4.28: 21398 4.28 - 4.90: 35763 Nonbonded interactions: 79550 Sorted by model distance: nonbonded pdb=" O1G ANP B 301 " pdb="MG MG B 302 " model vdw 1.817 2.170 nonbonded pdb=" O2B ANP B 301 " pdb="MG MG B 302 " model vdw 1.831 2.170 nonbonded pdb=" O1G ANP C 301 " pdb="MG MG C 302 " model vdw 1.876 2.170 nonbonded pdb=" OG SER C 50 " pdb="MG MG C 302 " model vdw 1.913 2.170 nonbonded pdb=" OG SER B 50 " pdb="MG MG B 302 " model vdw 1.920 2.170 ... (remaining 79545 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 'B' selection = chain 'C' } 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: 0.700 Set stop_for_unknowns flag: 0.010 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.130 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 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 0.035 9956 Z= 0.230 Angle : 0.642 10.187 13526 Z= 0.311 Chirality : 0.038 0.153 1565 Planarity : 0.004 0.032 1728 Dihedral : 15.241 84.544 3718 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.10 % Allowed : 21.51 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1250 helix: 2.54 (0.21), residues: 638 sheet: 0.04 (0.43), residues: 165 loop : -0.62 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.008 0.001 HIS A 558 PHE 0.015 0.001 PHE A 50 TYR 0.007 0.001 TYR A 197 ARG 0.003 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.12094 ( 565) hydrogen bonds : angle 5.67272 ( 1614) covalent geometry : bond 0.00495 ( 9956) covalent geometry : angle 0.64239 (13526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9756 (mt) cc_final: 0.9433 (mt) REVERT: A 87 MET cc_start: 0.9303 (tpp) cc_final: 0.9004 (tpp) REVERT: A 175 MET cc_start: 0.9422 (mmt) cc_final: 0.9090 (mmm) REVERT: A 176 MET cc_start: 0.8857 (ppp) cc_final: 0.8226 (ppp) REVERT: A 312 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 348 SER cc_start: 0.9525 (t) cc_final: 0.9009 (p) REVERT: A 398 MET cc_start: 0.8866 (tpp) cc_final: 0.8620 (tpp) REVERT: A 402 MET cc_start: 0.8604 (mmt) cc_final: 0.8273 (mmm) REVERT: A 424 MET cc_start: 0.8823 (tpp) cc_final: 0.8161 (tpp) REVERT: A 575 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8873 (tmm) REVERT: A 594 MET cc_start: 0.8516 (tpt) cc_final: 0.8268 (ppp) REVERT: A 691 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8541 (t) REVERT: A 771 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9123 (tp) REVERT: B 118 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: B 130 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9461 (tt) REVERT: C 103 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9098 (pp) outliers start: 32 outliers final: 22 residues processed: 90 average time/residue: 0.1863 time to fit residues: 25.5227 Evaluate side-chains 91 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.054934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037998 restraints weight = 45903.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.039419 restraints weight = 22394.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.040356 restraints weight = 14143.722| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9956 Z= 0.211 Angle : 0.590 6.698 13526 Z= 0.294 Chirality : 0.039 0.165 1565 Planarity : 0.004 0.043 1728 Dihedral : 8.518 81.604 1467 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.68 % Allowed : 20.25 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1250 helix: 2.92 (0.20), residues: 639 sheet: 0.02 (0.43), residues: 167 loop : -0.58 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 451 HIS 0.006 0.001 HIS A 558 PHE 0.013 0.001 PHE A 50 TYR 0.007 0.001 TYR A 209 ARG 0.005 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 565) hydrogen bonds : angle 4.40392 ( 1614) covalent geometry : bond 0.00459 ( 9956) covalent geometry : angle 0.59028 (13526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9752 (mt) cc_final: 0.9414 (mt) REVERT: A 175 MET cc_start: 0.9371 (mmt) cc_final: 0.8977 (mmm) REVERT: A 312 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8973 (tt) REVERT: A 398 MET cc_start: 0.8901 (tpp) cc_final: 0.8629 (tpp) REVERT: A 402 MET cc_start: 0.8613 (mmt) cc_final: 0.8293 (mmm) REVERT: A 424 MET cc_start: 0.8751 (tpp) cc_final: 0.8093 (tpp) REVERT: A 575 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8766 (tmm) REVERT: A 594 MET cc_start: 0.8488 (tpt) cc_final: 0.8133 (ppp) REVERT: A 691 CYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8413 (t) REVERT: A 739 SER cc_start: 0.9419 (OUTLIER) cc_final: 0.9054 (p) REVERT: C 103 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9138 (pp) outliers start: 38 outliers final: 22 residues processed: 97 average time/residue: 0.1874 time to fit residues: 27.7414 Evaluate side-chains 89 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.038524 restraints weight = 46279.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.039935 restraints weight = 21589.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.040869 restraints weight = 13263.382| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9956 Z= 0.197 Angle : 0.571 5.943 13526 Z= 0.283 Chirality : 0.038 0.145 1565 Planarity : 0.003 0.045 1728 Dihedral : 7.629 80.668 1441 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.55 % Allowed : 20.16 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1250 helix: 3.08 (0.20), residues: 642 sheet: 0.05 (0.43), residues: 166 loop : -0.58 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 641 HIS 0.007 0.001 HIS A 558 PHE 0.013 0.001 PHE A 50 TYR 0.006 0.001 TYR A 197 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 565) hydrogen bonds : angle 4.22520 ( 1614) covalent geometry : bond 0.00430 ( 9956) covalent geometry : angle 0.57125 (13526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 62 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9748 (mt) cc_final: 0.9391 (mt) REVERT: A 87 MET cc_start: 0.8879 (tpp) cc_final: 0.8550 (tpp) REVERT: A 175 MET cc_start: 0.9384 (mmt) cc_final: 0.9021 (mmm) REVERT: A 312 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8977 (tt) REVERT: A 350 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9557 (mm) REVERT: A 398 MET cc_start: 0.8882 (tpp) cc_final: 0.8601 (tpp) REVERT: A 402 MET cc_start: 0.8598 (mmt) cc_final: 0.8286 (mmm) REVERT: A 424 MET cc_start: 0.8744 (tpp) cc_final: 0.8078 (tpp) REVERT: A 575 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8759 (tmm) REVERT: A 691 CYS cc_start: 0.9058 (m) cc_final: 0.8752 (t) REVERT: A 739 SER cc_start: 0.9420 (OUTLIER) cc_final: 0.9051 (p) REVERT: B 44 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: C 103 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9133 (pp) outliers start: 47 outliers final: 25 residues processed: 107 average time/residue: 0.1752 time to fit residues: 28.6506 Evaluate side-chains 90 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.054791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.038376 restraints weight = 46126.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039790 restraints weight = 21588.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.040739 restraints weight = 13298.078| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9956 Z= 0.210 Angle : 0.587 6.416 13526 Z= 0.289 Chirality : 0.039 0.164 1565 Planarity : 0.003 0.047 1728 Dihedral : 7.563 81.579 1438 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.65 % Allowed : 20.74 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.25), residues: 1250 helix: 3.07 (0.20), residues: 644 sheet: -0.02 (0.43), residues: 166 loop : -0.58 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 641 HIS 0.007 0.001 HIS A 558 PHE 0.013 0.001 PHE A 50 TYR 0.007 0.001 TYR A 197 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 565) hydrogen bonds : angle 4.20590 ( 1614) covalent geometry : bond 0.00459 ( 9956) covalent geometry : angle 0.58663 (13526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 64 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9749 (mt) cc_final: 0.9389 (mt) REVERT: A 87 MET cc_start: 0.8929 (tpp) cc_final: 0.8641 (tpp) REVERT: A 170 MET cc_start: 0.8327 (tpp) cc_final: 0.7993 (tpp) REVERT: A 175 MET cc_start: 0.9386 (mmt) cc_final: 0.9097 (mmm) REVERT: A 312 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8981 (tt) REVERT: A 398 MET cc_start: 0.8896 (tpp) cc_final: 0.8610 (tpp) REVERT: A 402 MET cc_start: 0.8610 (mmt) cc_final: 0.8303 (mmm) REVERT: A 424 MET cc_start: 0.8753 (tpp) cc_final: 0.8096 (tpp) REVERT: A 575 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8774 (tmm) REVERT: A 691 CYS cc_start: 0.9027 (m) cc_final: 0.8823 (t) REVERT: A 739 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9050 (p) REVERT: B 44 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: C 103 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9128 (pp) outliers start: 48 outliers final: 27 residues processed: 107 average time/residue: 0.1964 time to fit residues: 31.7253 Evaluate side-chains 91 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.038834 restraints weight = 44952.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.040281 restraints weight = 21794.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.041255 restraints weight = 13601.256| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9956 Z= 0.142 Angle : 0.537 7.310 13526 Z= 0.269 Chirality : 0.038 0.304 1565 Planarity : 0.004 0.055 1728 Dihedral : 7.410 80.871 1438 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.26 % Allowed : 20.83 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1250 helix: 3.19 (0.20), residues: 643 sheet: -0.02 (0.43), residues: 164 loop : -0.50 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 641 HIS 0.007 0.001 HIS A 558 PHE 0.014 0.001 PHE A 50 TYR 0.007 0.001 TYR A 197 ARG 0.003 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 565) hydrogen bonds : angle 4.01415 ( 1614) covalent geometry : bond 0.00311 ( 9956) covalent geometry : angle 0.53698 (13526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 63 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9748 (mt) cc_final: 0.9388 (mt) REVERT: A 87 MET cc_start: 0.8929 (tpp) cc_final: 0.8620 (tpp) REVERT: A 170 MET cc_start: 0.8305 (tpp) cc_final: 0.7970 (tpp) REVERT: A 175 MET cc_start: 0.9357 (mmt) cc_final: 0.9053 (mmm) REVERT: A 312 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8976 (tt) REVERT: A 350 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9563 (mm) REVERT: A 398 MET cc_start: 0.8860 (tpp) cc_final: 0.8577 (tpp) REVERT: A 402 MET cc_start: 0.8563 (mmt) cc_final: 0.8258 (mmm) REVERT: A 424 MET cc_start: 0.8727 (tpp) cc_final: 0.8051 (tpp) REVERT: A 512 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: A 575 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8815 (tmm) REVERT: A 594 MET cc_start: 0.8016 (tpt) cc_final: 0.7691 (ppp) REVERT: A 739 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 44 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8535 (pm20) outliers start: 44 outliers final: 27 residues processed: 103 average time/residue: 0.1702 time to fit residues: 27.2364 Evaluate side-chains 92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 38 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 61 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.055714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.038656 restraints weight = 45105.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.040113 restraints weight = 21730.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041106 restraints weight = 13599.609| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9956 Z= 0.136 Angle : 0.525 6.099 13526 Z= 0.263 Chirality : 0.038 0.182 1565 Planarity : 0.003 0.046 1728 Dihedral : 7.064 79.969 1432 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.59 % Allowed : 21.71 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1250 helix: 3.18 (0.20), residues: 643 sheet: -0.04 (0.43), residues: 164 loop : -0.48 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 641 HIS 0.009 0.001 HIS A 512 PHE 0.014 0.001 PHE A 508 TYR 0.005 0.001 TYR A 197 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 565) hydrogen bonds : angle 3.99606 ( 1614) covalent geometry : bond 0.00298 ( 9956) covalent geometry : angle 0.52540 (13526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9754 (mt) cc_final: 0.9390 (mt) REVERT: A 87 MET cc_start: 0.8932 (tpp) cc_final: 0.8640 (tpp) REVERT: A 170 MET cc_start: 0.8345 (tpp) cc_final: 0.8006 (tpp) REVERT: A 175 MET cc_start: 0.9354 (mmt) cc_final: 0.9053 (mmm) REVERT: A 312 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8976 (tt) REVERT: A 398 MET cc_start: 0.8867 (tpp) cc_final: 0.8575 (tpp) REVERT: A 402 MET cc_start: 0.8563 (mmt) cc_final: 0.8257 (mmm) REVERT: A 424 MET cc_start: 0.8740 (tpp) cc_final: 0.8064 (tpp) REVERT: A 575 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8914 (tmm) REVERT: A 594 MET cc_start: 0.7972 (tpt) cc_final: 0.7639 (ppp) REVERT: A 739 SER cc_start: 0.9420 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 44 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: B 63 SER cc_start: 0.9627 (OUTLIER) cc_final: 0.9393 (p) REVERT: B 202 MET cc_start: 0.8699 (mpp) cc_final: 0.8204 (mpp) REVERT: C 202 MET cc_start: 0.8308 (mpp) cc_final: 0.8107 (mpp) outliers start: 37 outliers final: 27 residues processed: 94 average time/residue: 0.1727 time to fit residues: 25.9853 Evaluate side-chains 94 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.040144 restraints weight = 45142.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.041658 restraints weight = 21744.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042658 restraints weight = 13541.599| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9956 Z= 0.102 Angle : 0.512 8.300 13526 Z= 0.255 Chirality : 0.037 0.170 1565 Planarity : 0.003 0.059 1728 Dihedral : 6.797 75.580 1432 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.39 % Allowed : 21.71 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1250 helix: 3.23 (0.20), residues: 643 sheet: -0.03 (0.46), residues: 145 loop : -0.38 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 335 HIS 0.006 0.001 HIS A 558 PHE 0.014 0.001 PHE A 50 TYR 0.005 0.001 TYR A 520 ARG 0.004 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 565) hydrogen bonds : angle 3.82724 ( 1614) covalent geometry : bond 0.00214 ( 9956) covalent geometry : angle 0.51239 (13526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8795 (mm-30) REVERT: A 57 LEU cc_start: 0.9741 (mt) cc_final: 0.9379 (mt) REVERT: A 87 MET cc_start: 0.8997 (tpp) cc_final: 0.8673 (tpp) REVERT: A 170 MET cc_start: 0.8299 (tpp) cc_final: 0.7965 (tpp) REVERT: A 175 MET cc_start: 0.9337 (mmt) cc_final: 0.9020 (mmm) REVERT: A 398 MET cc_start: 0.8824 (tpp) cc_final: 0.8553 (tpp) REVERT: A 402 MET cc_start: 0.8519 (mmt) cc_final: 0.8207 (mmm) REVERT: A 424 MET cc_start: 0.8750 (tpp) cc_final: 0.8094 (tpp) REVERT: A 432 MET cc_start: 0.8151 (tpp) cc_final: 0.7750 (tpp) REVERT: A 575 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9023 (ttp) REVERT: A 594 MET cc_start: 0.7936 (tpt) cc_final: 0.7566 (ppp) REVERT: A 739 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9066 (p) REVERT: B 44 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: B 63 SER cc_start: 0.9623 (OUTLIER) cc_final: 0.9402 (p) REVERT: B 202 MET cc_start: 0.8698 (mpp) cc_final: 0.8375 (mpp) REVERT: C 90 VAL cc_start: 0.9544 (t) cc_final: 0.9270 (p) REVERT: C 202 MET cc_start: 0.8431 (mpp) cc_final: 0.8210 (mpp) outliers start: 35 outliers final: 21 residues processed: 104 average time/residue: 0.1892 time to fit residues: 30.6005 Evaluate side-chains 92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 0.0270 overall best weight: 1.0052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.040298 restraints weight = 45366.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.041823 restraints weight = 21859.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042859 restraints weight = 13601.662| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9956 Z= 0.106 Angle : 0.533 8.557 13526 Z= 0.262 Chirality : 0.038 0.399 1565 Planarity : 0.003 0.045 1728 Dihedral : 6.659 74.453 1430 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.20 % Allowed : 22.00 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.25), residues: 1250 helix: 3.18 (0.20), residues: 643 sheet: 0.05 (0.46), residues: 147 loop : -0.37 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 195 HIS 0.007 0.001 HIS A 558 PHE 0.014 0.001 PHE A 50 TYR 0.007 0.001 TYR A 520 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 565) hydrogen bonds : angle 3.87112 ( 1614) covalent geometry : bond 0.00227 ( 9956) covalent geometry : angle 0.53299 (13526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8810 (mm-30) REVERT: A 57 LEU cc_start: 0.9750 (mt) cc_final: 0.9386 (mt) REVERT: A 87 MET cc_start: 0.9007 (tpp) cc_final: 0.8712 (tpp) REVERT: A 170 MET cc_start: 0.8307 (tpp) cc_final: 0.7969 (tpp) REVERT: A 175 MET cc_start: 0.9340 (mmt) cc_final: 0.9017 (mmm) REVERT: A 398 MET cc_start: 0.8811 (tpp) cc_final: 0.8527 (tpp) REVERT: A 402 MET cc_start: 0.8501 (mmt) cc_final: 0.8190 (mmm) REVERT: A 424 MET cc_start: 0.8765 (tpp) cc_final: 0.8084 (tpp) REVERT: A 432 MET cc_start: 0.8115 (tpp) cc_final: 0.7802 (tpp) REVERT: A 575 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9005 (ttp) REVERT: A 594 MET cc_start: 0.7924 (tpt) cc_final: 0.7544 (ppp) REVERT: A 739 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9061 (p) REVERT: B 44 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: B 63 SER cc_start: 0.9622 (OUTLIER) cc_final: 0.9404 (p) REVERT: B 202 MET cc_start: 0.8685 (mpp) cc_final: 0.8370 (mpp) REVERT: C 90 VAL cc_start: 0.9532 (t) cc_final: 0.9247 (p) REVERT: C 202 MET cc_start: 0.8417 (mpp) cc_final: 0.8162 (mpp) outliers start: 33 outliers final: 24 residues processed: 98 average time/residue: 0.1768 time to fit residues: 27.4276 Evaluate side-chains 93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 9.9990 chunk 48 optimal weight: 0.0670 chunk 118 optimal weight: 0.0010 chunk 115 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.041022 restraints weight = 44899.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.042572 restraints weight = 21605.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043599 restraints weight = 13361.890| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9956 Z= 0.103 Angle : 0.540 11.492 13526 Z= 0.264 Chirality : 0.038 0.220 1565 Planarity : 0.003 0.062 1728 Dihedral : 6.465 71.405 1430 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.81 % Allowed : 22.48 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.25), residues: 1250 helix: 3.16 (0.20), residues: 643 sheet: 0.25 (0.46), residues: 145 loop : -0.39 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 195 HIS 0.006 0.001 HIS A 558 PHE 0.013 0.001 PHE A 50 TYR 0.006 0.001 TYR A 520 ARG 0.003 0.000 ARG A 707 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 565) hydrogen bonds : angle 3.84472 ( 1614) covalent geometry : bond 0.00220 ( 9956) covalent geometry : angle 0.54040 (13526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8836 (mm-30) REVERT: A 57 LEU cc_start: 0.9753 (mt) cc_final: 0.9395 (mt) REVERT: A 87 MET cc_start: 0.9040 (tpp) cc_final: 0.8735 (tpp) REVERT: A 170 MET cc_start: 0.8283 (tpp) cc_final: 0.7950 (tpp) REVERT: A 175 MET cc_start: 0.9346 (mmt) cc_final: 0.9008 (mmm) REVERT: A 348 SER cc_start: 0.9358 (t) cc_final: 0.8959 (p) REVERT: A 398 MET cc_start: 0.8774 (tpp) cc_final: 0.8495 (tpp) REVERT: A 402 MET cc_start: 0.8458 (mmt) cc_final: 0.8151 (mmm) REVERT: A 424 MET cc_start: 0.8756 (tpp) cc_final: 0.8068 (tpp) REVERT: A 432 MET cc_start: 0.8085 (tpp) cc_final: 0.7781 (tpp) REVERT: A 575 MET cc_start: 0.9364 (ttm) cc_final: 0.9017 (tmm) REVERT: A 594 MET cc_start: 0.7952 (tpt) cc_final: 0.7540 (ppp) REVERT: A 739 SER cc_start: 0.9371 (OUTLIER) cc_final: 0.9059 (p) REVERT: B 44 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: B 202 MET cc_start: 0.8695 (mpp) cc_final: 0.8469 (mpp) REVERT: C 90 VAL cc_start: 0.9482 (t) cc_final: 0.9172 (p) REVERT: C 202 MET cc_start: 0.8392 (mpp) cc_final: 0.8143 (mpp) outliers start: 29 outliers final: 21 residues processed: 96 average time/residue: 0.1883 time to fit residues: 28.1546 Evaluate side-chains 90 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.038931 restraints weight = 45614.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.040371 restraints weight = 22239.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041356 restraints weight = 13990.042| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9956 Z= 0.208 Angle : 0.628 11.777 13526 Z= 0.301 Chirality : 0.039 0.192 1565 Planarity : 0.003 0.042 1728 Dihedral : 6.222 72.587 1422 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.52 % Allowed : 22.77 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1250 helix: 3.24 (0.20), residues: 643 sheet: 0.13 (0.43), residues: 167 loop : -0.41 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 195 HIS 0.007 0.001 HIS A 558 PHE 0.020 0.001 PHE A 243 TYR 0.007 0.001 TYR A 197 ARG 0.003 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 565) hydrogen bonds : angle 4.06507 ( 1614) covalent geometry : bond 0.00456 ( 9956) covalent geometry : angle 0.62811 (13526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9758 (mt) cc_final: 0.9390 (mt) REVERT: A 170 MET cc_start: 0.8361 (tpp) cc_final: 0.8147 (tpp) REVERT: A 175 MET cc_start: 0.9371 (mmt) cc_final: 0.9037 (mmm) REVERT: A 350 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9508 (mm) REVERT: A 398 MET cc_start: 0.8888 (tpp) cc_final: 0.8582 (tpp) REVERT: A 402 MET cc_start: 0.8574 (mmt) cc_final: 0.8262 (mmm) REVERT: A 424 MET cc_start: 0.8776 (tpp) cc_final: 0.8115 (tpp) REVERT: A 432 MET cc_start: 0.8174 (tpp) cc_final: 0.7973 (tpp) REVERT: A 575 MET cc_start: 0.9349 (ttm) cc_final: 0.9046 (ttp) REVERT: A 594 MET cc_start: 0.7908 (tpt) cc_final: 0.7530 (ppp) REVERT: A 739 SER cc_start: 0.9398 (OUTLIER) cc_final: 0.9046 (p) REVERT: B 202 MET cc_start: 0.8701 (mpp) cc_final: 0.8368 (mpp) REVERT: C 90 VAL cc_start: 0.9597 (t) cc_final: 0.9348 (p) outliers start: 26 outliers final: 20 residues processed: 88 average time/residue: 0.1691 time to fit residues: 23.4449 Evaluate side-chains 84 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.057105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040034 restraints weight = 44791.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.041579 restraints weight = 21663.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042605 restraints weight = 13300.992| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9956 Z= 0.110 Angle : 0.572 11.012 13526 Z= 0.277 Chirality : 0.038 0.177 1565 Planarity : 0.003 0.060 1728 Dihedral : 6.146 72.177 1422 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.03 % Allowed : 23.45 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1250 helix: 3.25 (0.20), residues: 643 sheet: 0.21 (0.46), residues: 145 loop : -0.38 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 770 HIS 0.006 0.001 HIS A 558 PHE 0.013 0.001 PHE A 50 TYR 0.005 0.001 TYR A 520 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 565) hydrogen bonds : angle 3.87057 ( 1614) covalent geometry : bond 0.00243 ( 9956) covalent geometry : angle 0.57232 (13526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.42 seconds wall clock time: 53 minutes 31.33 seconds (3211.33 seconds total)