Starting phenix.real_space_refine on Fri Sep 11 13:30:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.map" model { file = "/net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ac_75023/09_2026/10ac_75023.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 3 5.16 5 C 5859 2.51 5 N 1542 2.21 5 O 1863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9270 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3089 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 397} Chain: "B" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3089 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 397} Chain: "C" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3089 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 397} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.20 Number of scatterers: 9270 At special positions: 0 Unit cell: (108.07, 110.21, 73.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 3 16.00 O 1863 8.00 N 1542 7.00 C 5859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 325.8 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 7.7% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.642A pdb=" N ILE A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.749A pdb=" N ILE A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 removed outlier: 4.323A pdb=" N GLN A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 175' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.563A pdb=" N THR A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.660A pdb=" N ILE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.741A pdb=" N ILE B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.195A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 175' Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.677A pdb=" N THR B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.661A pdb=" N ILE C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.804A pdb=" N ILE C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 4.290A pdb=" N GLN C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 175' Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.516A pdb=" N THR C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 7.182A pdb=" N GLY A 45 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS A 61 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS A 81 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 114 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 83 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 112 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN A 85 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 11.909A pdb=" N ARG A 110 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN A 131 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL A 145 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 169 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 147 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA3, first strand: chain 'B' and resid 210 through 212 removed outlier: 5.888A pdb=" N ASN B 273 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 296 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLU B 299 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ASP B 332 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS B 81 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 114 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 83 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 112 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN B 85 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N ARG B 110 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLN B 131 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 145 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 169 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 147 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 210 through 212 removed outlier: 7.155A pdb=" N GLY C 45 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS C 61 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 81 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 114 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE C 83 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 112 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN C 85 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N ARG C 110 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN C 131 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 145 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE C 169 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 147 " --> pdb=" O ASP C 167 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3104 1.34 - 1.46: 2066 1.46 - 1.57: 4283 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 9459 Sorted by residual: bond pdb=" C GLY B 208 " pdb=" N SER B 209 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.28e-02 6.10e+03 8.39e-01 bond pdb=" C PHE A 338 " pdb=" N GLY A 339 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.07e-01 bond pdb=" C PHE C 338 " pdb=" N GLY C 339 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.41e-01 bond pdb=" C PHE B 338 " pdb=" N GLY B 339 " ideal model delta sigma weight residual 1.331 1.320 0.011 1.46e-02 4.69e+03 5.52e-01 bond pdb=" CA GLY B 143 " pdb=" C GLY B 143 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.29e-02 6.01e+03 4.97e-01 ... (remaining 9454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 12183 1.03 - 2.07: 581 2.07 - 3.10: 64 3.10 - 4.14: 14 4.14 - 5.17: 7 Bond angle restraints: 12849 Sorted by residual: angle pdb=" CA SER A 387 " pdb=" C SER A 387 " pdb=" N PRO A 388 " ideal model delta sigma weight residual 117.68 119.55 -1.87 7.10e-01 1.98e+00 6.93e+00 angle pdb=" CA GLY A 94 " pdb=" C GLY A 94 " pdb=" N TYR A 95 " ideal model delta sigma weight residual 114.75 117.32 -2.57 9.90e-01 1.02e+00 6.76e+00 angle pdb=" CA SER C 387 " pdb=" C SER C 387 " pdb=" N PRO C 388 " ideal model delta sigma weight residual 117.68 119.52 -1.84 7.10e-01 1.98e+00 6.69e+00 angle pdb=" CA GLY C 94 " pdb=" C GLY C 94 " pdb=" N TYR C 95 " ideal model delta sigma weight residual 114.75 117.21 -2.46 9.90e-01 1.02e+00 6.17e+00 angle pdb=" CA GLY B 94 " pdb=" C GLY B 94 " pdb=" N TYR B 95 " ideal model delta sigma weight residual 114.75 117.12 -2.37 9.90e-01 1.02e+00 5.73e+00 ... (remaining 12844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5144 16.67 - 33.35: 188 33.35 - 50.02: 43 50.02 - 66.70: 19 66.70 - 83.37: 6 Dihedral angle restraints: 5400 sinusoidal: 1971 harmonic: 3429 Sorted by residual: dihedral pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " pdb=" CD GLU A 180 " ideal model delta sinusoidal sigma weight residual 60.00 119.40 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU C 180 " pdb=" CB GLU C 180 " pdb=" CG GLU C 180 " pdb=" CD GLU C 180 " ideal model delta sinusoidal sigma weight residual 60.00 119.23 -59.23 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASP C 332 " pdb=" CA ASP C 332 " pdb=" CB ASP C 332 " pdb=" CG ASP C 332 " ideal model delta sinusoidal sigma weight residual -180.00 -121.41 -58.59 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 755 0.026 - 0.052: 388 0.052 - 0.077: 140 0.077 - 0.103: 52 0.103 - 0.129: 57 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ILE B 337 " pdb=" N ILE B 337 " pdb=" C ILE B 337 " pdb=" CB ILE B 337 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE C 337 " pdb=" N ILE C 337 " pdb=" C ILE C 337 " pdb=" CB ILE C 337 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE C 126 " pdb=" N ILE C 126 " pdb=" C ILE C 126 " pdb=" CB ILE C 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1389 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 387 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO C 388 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 387 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 388 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 387 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 388 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.022 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1219 2.76 - 3.29: 7654 3.29 - 3.83: 14709 3.83 - 4.36: 17612 4.36 - 4.90: 33416 Nonbonded interactions: 74610 Sorted by model distance: nonbonded pdb=" OD2 ASP C 142 " pdb="CA CA C 501 " model vdw 2.219 2.510 nonbonded pdb=" OD2 ASP B 142 " pdb="CA CA B 501 " model vdw 2.221 2.510 nonbonded pdb=" OE2 GLU A 307 " pdb="CA CA A 501 " model vdw 2.231 2.510 nonbonded pdb=" OG SER C 289 " pdb=" OG1 THR C 342 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 142 " pdb="CA CA A 501 " model vdw 2.233 2.510 ... (remaining 74605 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.004 0.019 9459 Z= 0.176 Angle : 0.509 5.173 12849 Z= 0.310 Chirality : 0.041 0.129 1392 Planarity : 0.003 0.040 1704 Dihedral : 10.784 83.374 3246 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.79 % Allowed : 3.36 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1200 helix: -4.43 (0.75), residues: 18 sheet: 1.02 (0.20), residues: 717 loop : -1.26 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 335 TYR 0.011 0.001 TYR A 113 PHE 0.018 0.002 PHE A 395 TRP 0.006 0.001 TRP A 249 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 9459) covalent geometry : angle 0.50858 / 0.31 (12849) hydrogen bonds : bond 0.19340 / 12.48 ( 571) hydrogen bonds : angle 7.92512 / 5.49 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.262 Fit side-chains REVERT: B 81 LYS cc_start: 0.8162 (mttt) cc_final: 0.7894 (mttp) REVERT: C 320 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 423 LYS cc_start: 0.8446 (mttt) cc_final: 0.8246 (mttp) outliers start: 17 outliers final: 7 residues processed: 114 average time/residue: 0.6986 time to fit residues: 84.2600 Evaluate side-chains 71 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 368 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 HIS A 189 ASN A 216 GLN B 181 HIS B 216 GLN C 181 HIS C 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.061077 restraints weight = 14708.191| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.45 r_work: 0.2517 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 9459 Z= 0.220 Angle : 0.579 6.342 12849 Z= 0.332 Chirality : 0.044 0.141 1392 Planarity : 0.003 0.041 1704 Dihedral : 5.726 57.395 1321 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.21 % Allowed : 5.99 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1200 helix: -4.16 (0.86), residues: 18 sheet: 1.21 (0.19), residues: 714 loop : -1.11 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 335 TYR 0.014 0.002 TYR A 113 PHE 0.021 0.002 PHE A 395 TRP 0.008 0.001 TRP C 222 HIS 0.005 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 ( 9459) covalent geometry : angle 0.57878 / 0.33 (12849) hydrogen bonds : bond 0.04764 / 3.15 ( 571) hydrogen bonds : angle 5.26326 / 3.57 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.365 Fit side-chains REVERT: A 180 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: B 81 LYS cc_start: 0.8931 (mttt) cc_final: 0.8731 (mttp) REVERT: B 180 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: B 423 LYS cc_start: 0.9138 (mttt) cc_final: 0.8907 (mttm) REVERT: C 180 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: C 283 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8511 (p) REVERT: C 332 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8684 (m-30) outliers start: 21 outliers final: 10 residues processed: 75 average time/residue: 0.6113 time to fit residues: 49.0492 Evaluate side-chains 58 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN C 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.060214 restraints weight = 14661.588| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.46 r_work: 0.2539 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 9459 Z= 0.255 Angle : 0.592 6.685 12849 Z= 0.338 Chirality : 0.044 0.143 1392 Planarity : 0.003 0.043 1704 Dihedral : 5.582 57.908 1312 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.31 % Allowed : 7.05 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1200 helix: -4.02 (0.91), residues: 18 sheet: 1.35 (0.19), residues: 690 loop : -1.00 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 335 TYR 0.014 0.002 TYR A 113 PHE 0.022 0.002 PHE A 395 TRP 0.007 0.001 TRP C 222 HIS 0.005 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.26 ( 9459) covalent geometry : angle 0.59199 / 0.34 (12849) hydrogen bonds : bond 0.04647 / 3.06 ( 571) hydrogen bonds : angle 5.12025 / 3.46 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.404 Fit side-chains REVERT: A 180 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: B 377 GLU cc_start: 0.9312 (tt0) cc_final: 0.9101 (tt0) REVERT: B 423 LYS cc_start: 0.9132 (mttt) cc_final: 0.8903 (mttm) REVERT: C 377 GLU cc_start: 0.9314 (tt0) cc_final: 0.9017 (tt0) outliers start: 22 outliers final: 10 residues processed: 68 average time/residue: 0.6816 time to fit residues: 49.4063 Evaluate side-chains 56 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.061473 restraints weight = 14692.581| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.48 r_work: 0.2568 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9459 Z= 0.161 Angle : 0.533 6.725 12849 Z= 0.306 Chirality : 0.042 0.139 1392 Planarity : 0.003 0.043 1704 Dihedral : 5.294 57.100 1310 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 8.62 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1200 helix: -3.76 (1.02), residues: 18 sheet: 1.32 (0.19), residues: 690 loop : -0.90 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.013 0.001 TYR A 113 PHE 0.019 0.002 PHE A 395 TRP 0.006 0.001 TRP C 222 HIS 0.003 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9459) covalent geometry : angle 0.53304 / 0.31 (12849) hydrogen bonds : bond 0.03918 / 2.58 ( 571) hydrogen bonds : angle 4.94973 / 3.34 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.359 Fit side-chains REVERT: A 92 ASP cc_start: 0.8151 (m-30) cc_final: 0.7619 (t0) REVERT: A 180 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: A 216 GLN cc_start: 0.8434 (tt0) cc_final: 0.8081 (mm-40) REVERT: A 349 GLU cc_start: 0.8653 (mp0) cc_final: 0.8312 (mm-30) REVERT: B 92 ASP cc_start: 0.7771 (m-30) cc_final: 0.7556 (m-30) REVERT: B 170 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9124 (mtt) REVERT: B 180 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: B 216 GLN cc_start: 0.8456 (tt0) cc_final: 0.7888 (mm-40) REVERT: B 423 LYS cc_start: 0.9127 (mttt) cc_final: 0.8891 (mttm) REVERT: C 332 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8632 (m-30) outliers start: 17 outliers final: 9 residues processed: 63 average time/residue: 0.6189 time to fit residues: 41.8408 Evaluate side-chains 58 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 109 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.061796 restraints weight = 14559.485| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.46 r_work: 0.2564 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 9459 Z= 0.159 Angle : 0.520 5.813 12849 Z= 0.299 Chirality : 0.042 0.139 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.229 57.189 1310 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.68 % Allowed : 9.04 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1200 helix: -3.50 (1.13), residues: 18 sheet: 1.31 (0.19), residues: 690 loop : -0.93 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.012 0.001 TYR A 113 PHE 0.019 0.002 PHE A 395 TRP 0.006 0.001 TRP C 222 HIS 0.003 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9459) covalent geometry : angle 0.51987 / 0.30 (12849) hydrogen bonds : bond 0.03787 / 2.49 ( 571) hydrogen bonds : angle 4.86350 / 3.28 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.252 Fit side-chains REVERT: A 92 ASP cc_start: 0.8066 (m-30) cc_final: 0.7673 (t0) REVERT: A 180 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 216 GLN cc_start: 0.8362 (tt0) cc_final: 0.8014 (mm-40) REVERT: A 349 GLU cc_start: 0.8635 (mp0) cc_final: 0.8199 (mm-30) REVERT: B 92 ASP cc_start: 0.7760 (m-30) cc_final: 0.7541 (m-30) REVERT: B 170 MET cc_start: 0.9345 (ttm) cc_final: 0.9114 (mtt) REVERT: B 216 GLN cc_start: 0.8394 (tt0) cc_final: 0.7808 (mm-40) REVERT: B 409 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7771 (mp0) REVERT: B 423 LYS cc_start: 0.9111 (mttt) cc_final: 0.8868 (mttm) REVERT: C 194 LYS cc_start: 0.8826 (mttp) cc_final: 0.8567 (mtpm) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.5904 time to fit residues: 40.1022 Evaluate side-chains 58 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.080653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.061403 restraints weight = 14715.012| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.50 r_work: 0.2553 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9459 Z= 0.177 Angle : 0.531 6.039 12849 Z= 0.304 Chirality : 0.042 0.140 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.282 57.254 1310 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.00 % Allowed : 9.15 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1200 helix: -3.38 (1.17), residues: 18 sheet: 1.33 (0.19), residues: 690 loop : -0.95 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.012 0.001 TYR A 113 PHE 0.020 0.002 PHE A 395 TRP 0.005 0.001 TRP C 222 HIS 0.003 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9459) covalent geometry : angle 0.53083 / 0.30 (12849) hydrogen bonds : bond 0.03857 / 2.53 ( 571) hydrogen bonds : angle 4.87029 / 3.29 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.356 Fit side-chains REVERT: A 180 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: A 216 GLN cc_start: 0.8368 (tt0) cc_final: 0.8037 (mm-40) REVERT: A 349 GLU cc_start: 0.8669 (mp0) cc_final: 0.8218 (mm-30) REVERT: A 383 ASP cc_start: 0.8596 (t70) cc_final: 0.8384 (OUTLIER) REVERT: B 170 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9123 (mtt) REVERT: B 216 GLN cc_start: 0.8404 (tt0) cc_final: 0.7838 (mm-40) REVERT: B 423 LYS cc_start: 0.9124 (mttt) cc_final: 0.8883 (mttm) REVERT: C 180 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: C 194 LYS cc_start: 0.8856 (mttp) cc_final: 0.8599 (mtpm) REVERT: C 267 LYS cc_start: 0.8975 (mtmm) cc_final: 0.8462 (pttm) outliers start: 19 outliers final: 13 residues processed: 64 average time/residue: 0.5981 time to fit residues: 41.0603 Evaluate side-chains 61 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 ASN C 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.081047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.061873 restraints weight = 14718.543| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.50 r_work: 0.2574 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9459 Z= 0.150 Angle : 0.512 5.726 12849 Z= 0.294 Chirality : 0.042 0.137 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.208 56.897 1310 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.37 % Allowed : 10.09 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1200 helix: -3.32 (1.18), residues: 18 sheet: 1.34 (0.19), residues: 690 loop : -0.93 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.011 0.001 TYR A 113 PHE 0.019 0.002 PHE A 395 TRP 0.006 0.001 TRP C 222 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9459) covalent geometry : angle 0.51211 / 0.29 (12849) hydrogen bonds : bond 0.03658 / 2.41 ( 571) hydrogen bonds : angle 4.82696 / 3.26 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.260 Fit side-chains REVERT: A 216 GLN cc_start: 0.8427 (tt0) cc_final: 0.8111 (mm-40) REVERT: A 349 GLU cc_start: 0.8626 (mp0) cc_final: 0.8126 (mm-30) REVERT: B 170 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9148 (mtt) REVERT: B 216 GLN cc_start: 0.8493 (tt0) cc_final: 0.7928 (mm-40) REVERT: B 423 LYS cc_start: 0.9123 (mttt) cc_final: 0.8890 (mttm) REVERT: C 180 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: C 194 LYS cc_start: 0.8851 (mttp) cc_final: 0.8598 (mtpm) REVERT: C 267 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8446 (pttm) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.5744 time to fit residues: 35.3500 Evaluate side-chains 58 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.060063 restraints weight = 14764.935| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.47 r_work: 0.2538 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 9459 Z= 0.241 Angle : 0.575 6.762 12849 Z= 0.327 Chirality : 0.044 0.141 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.508 57.790 1310 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 9.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1200 helix: -3.38 (1.15), residues: 18 sheet: 1.32 (0.19), residues: 690 loop : -1.05 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 328 TYR 0.013 0.002 TYR A 113 PHE 0.022 0.002 PHE A 395 TRP 0.005 0.001 TRP C 222 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 ( 9459) covalent geometry : angle 0.57543 / 0.33 (12849) hydrogen bonds : bond 0.04223 / 2.77 ( 571) hydrogen bonds : angle 4.93430 / 3.34 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.7893 (mm110) cc_final: 0.7362 (mp10) REVERT: A 216 GLN cc_start: 0.8425 (tt0) cc_final: 0.8068 (mm-40) REVERT: A 349 GLU cc_start: 0.8624 (mp0) cc_final: 0.8133 (mm-30) REVERT: B 27 GLU cc_start: 0.8626 (tp30) cc_final: 0.8370 (tp30) REVERT: B 170 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9072 (mtt) REVERT: B 216 GLN cc_start: 0.8518 (tt0) cc_final: 0.7950 (mm-40) REVERT: C 180 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7503 (tp30) outliers start: 19 outliers final: 15 residues processed: 57 average time/residue: 0.5815 time to fit residues: 35.7894 Evaluate side-chains 60 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.063189 restraints weight = 14582.184| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.45 r_work: 0.2572 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9459 Z= 0.106 Angle : 0.485 5.011 12849 Z= 0.279 Chirality : 0.042 0.135 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.058 56.253 1310 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.16 % Allowed : 10.41 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1200 helix: -3.11 (1.26), residues: 18 sheet: 1.35 (0.19), residues: 693 loop : -0.86 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.010 0.001 TYR A 113 PHE 0.018 0.001 PHE A 395 TRP 0.007 0.001 TRP C 222 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9459) covalent geometry : angle 0.48494 / 0.28 (12849) hydrogen bonds : bond 0.03273 / 2.16 ( 571) hydrogen bonds : angle 4.75668 / 3.22 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.408 Fit side-chains REVERT: A 180 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 216 GLN cc_start: 0.8385 (tt0) cc_final: 0.8016 (mm-40) REVERT: A 349 GLU cc_start: 0.8591 (mp0) cc_final: 0.8072 (mm-30) REVERT: B 27 GLU cc_start: 0.8626 (tp30) cc_final: 0.8338 (tp30) REVERT: B 170 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9078 (mtt) REVERT: B 216 GLN cc_start: 0.8455 (tt0) cc_final: 0.7832 (mm-40) REVERT: B 409 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7855 (mp0) REVERT: B 423 LYS cc_start: 0.9099 (mttt) cc_final: 0.8866 (mttm) REVERT: C 332 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8589 (m-30) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.6159 time to fit residues: 39.6866 Evaluate side-chains 53 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.081197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.062054 restraints weight = 14708.562| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.49 r_work: 0.2547 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9459 Z= 0.137 Angle : 0.506 5.681 12849 Z= 0.289 Chirality : 0.042 0.139 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.119 56.785 1310 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.95 % Allowed : 11.04 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1200 helix: -3.11 (1.24), residues: 18 sheet: 1.37 (0.19), residues: 690 loop : -0.87 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.011 0.001 TYR A 113 PHE 0.019 0.002 PHE A 395 TRP 0.006 0.001 TRP C 222 HIS 0.003 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9459) covalent geometry : angle 0.50645 / 0.29 (12849) hydrogen bonds : bond 0.03483 / 2.29 ( 571) hydrogen bonds : angle 4.74268 / 3.21 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.243 Fit side-chains REVERT: A 180 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 216 GLN cc_start: 0.8418 (tt0) cc_final: 0.8050 (mm-40) REVERT: A 349 GLU cc_start: 0.8621 (mp0) cc_final: 0.8102 (mm-30) REVERT: B 27 GLU cc_start: 0.8634 (tp30) cc_final: 0.8345 (tp30) REVERT: B 170 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9117 (mtt) REVERT: B 216 GLN cc_start: 0.8476 (tt0) cc_final: 0.7903 (mm-40) REVERT: B 409 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7872 (mp0) REVERT: B 423 LYS cc_start: 0.9134 (mttt) cc_final: 0.8910 (mttm) REVERT: C 49 LYS cc_start: 0.9334 (ttpp) cc_final: 0.9120 (tppt) REVERT: C 267 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8435 (pttm) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.6027 time to fit residues: 34.4397 Evaluate side-chains 54 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.062185 restraints weight = 14612.767| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.49 r_work: 0.2543 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9459 Z= 0.135 Angle : 0.508 5.554 12849 Z= 0.289 Chirality : 0.042 0.138 1392 Planarity : 0.003 0.042 1704 Dihedral : 5.109 56.549 1310 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.05 % Allowed : 11.15 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1200 helix: -3.12 (1.23), residues: 18 sheet: 1.36 (0.19), residues: 690 loop : -0.87 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.011 0.001 TYR A 113 PHE 0.019 0.002 PHE A 395 TRP 0.006 0.001 TRP C 222 HIS 0.003 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9459) covalent geometry : angle 0.50781 / 0.29 (12849) hydrogen bonds : bond 0.03445 / 2.27 ( 571) hydrogen bonds : angle 4.73721 / 3.21 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.26 seconds wall clock time: 47 minutes 50.19 seconds (2870.19 seconds total)