Starting phenix.real_space_refine on Thu Jul 2 03:31:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ero_28556/07_2026/8ero_28556.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.191 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 8 5.49 5 Mg 4 5.21 5 S 50 5.16 5 C 4156 2.51 5 N 892 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6154 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "B" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-1': 11, 'LBN:plan-2': 11, 'LBN:plan-3': 12} Unresolved non-hydrogen planarities: 116 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-1': 11, 'LBN:plan-2': 11, 'LBN:plan-3': 12} Unresolved non-hydrogen planarities: 116 Time building chain proxies: 1.49, per 1000 atoms: 0.24 Number of scatterers: 6154 At special positions: 0 Unit cell: (78.1, 122.1, 70.4, 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 50 16.00 P 8 15.00 Mg 4 11.99 O 1044 8.00 N 892 7.00 C 4156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 336.7 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 76.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.773A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.564A pdb=" N MET A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 Processing helix chain 'A' and resid 86 through 89 removed outlier: 4.030A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 93 through 120 removed outlier: 3.800A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 152 removed outlier: 3.956A pdb=" N GLU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 160 through 181 removed outlier: 4.121A pdb=" N CYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 3.510A pdb=" N LEU A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.953A pdb=" N TRP A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 249 removed outlier: 3.528A pdb=" N LEU A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.616A pdb=" N PHE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 378 removed outlier: 3.863A pdb=" N TRP A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.763A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.564A pdb=" N MET B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 85 Processing helix chain 'B' and resid 86 through 89 removed outlier: 4.030A pdb=" N THR B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 93 through 120 removed outlier: 3.800A pdb=" N TYR B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 152 removed outlier: 3.956A pdb=" N GLU B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 160 through 181 removed outlier: 4.121A pdb=" N CYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.510A pdb=" N LEU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.953A pdb=" N TRP B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 249 removed outlier: 3.528A pdb=" N LEU B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 293 through 318 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.616A pdb=" N PHE B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 378 removed outlier: 3.863A pdb=" N TRP B 352 " --> pdb=" O TYR B 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 38 406 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 892 1.32 - 1.44: 1631 1.44 - 1.56: 3663 1.56 - 1.69: 14 1.69 - 1.81: 74 Bond restraints: 6274 Sorted by residual: bond pdb=" O2 LBN B 515 " pdb=" P1 LBN B 515 " ideal model delta sigma weight residual 1.650 1.482 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" O2 LBN A 512 " pdb=" P1 LBN A 512 " ideal model delta sigma weight residual 1.650 1.482 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" O3A CDP B 516 " pdb=" PB CDP B 516 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" O3A CDP A 513 " pdb=" PB CDP A 513 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" O4 LBN A 512 " pdb=" P1 LBN A 512 " ideal model delta sigma weight residual 1.497 1.596 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 6269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 8327 3.12 - 6.23: 63 6.23 - 9.35: 14 9.35 - 12.47: 10 12.47 - 15.59: 2 Bond angle restraints: 8416 Sorted by residual: angle pdb=" O1 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O2 LBN B 515 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O1 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O2 LBN A 512 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O3 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O4 LBN A 512 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O4 LBN B 515 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O1 LBN B 507 " pdb=" P1 LBN B 507 " pdb=" O2 LBN B 507 " ideal model delta sigma weight residual 93.45 104.29 -10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 8411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.32: 3498 26.32 - 52.65: 186 52.65 - 78.97: 36 78.97 - 105.29: 4 105.29 - 131.62: 22 Dihedral angle restraints: 3746 sinusoidal: 1644 harmonic: 2102 Sorted by residual: dihedral pdb=" C32 LBN A 509 " pdb=" C33 LBN A 509 " pdb=" C4 LBN A 509 " pdb=" C7 LBN A 509 " ideal model delta sinusoidal sigma weight residual 179.89 -48.49 -131.62 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C32 LBN B 512 " pdb=" C33 LBN B 512 " pdb=" C4 LBN B 512 " pdb=" C7 LBN B 512 " ideal model delta sinusoidal sigma weight residual 179.89 -48.49 -131.62 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C32 LBN A 506 " pdb=" C33 LBN A 506 " pdb=" C4 LBN A 506 " pdb=" C7 LBN A 506 " ideal model delta sinusoidal sigma weight residual 179.89 55.90 123.99 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 3743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 762 0.052 - 0.103: 158 0.103 - 0.155: 26 0.155 - 0.206: 0 0.206 - 0.258: 4 Chirality restraints: 950 Sorted by residual: chirality pdb=" C3' CDP A 513 " pdb=" C2' CDP A 513 " pdb=" C4' CDP A 513 " pdb=" O3' CDP A 513 " both_signs ideal model delta sigma weight residual False -2.38 -2.64 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C3' CDP B 516 " pdb=" C2' CDP B 516 " pdb=" C4' CDP B 516 " pdb=" O3' CDP B 516 " both_signs ideal model delta sigma weight residual False -2.38 -2.64 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C2 LBN A 504 " pdb=" C1 LBN A 504 " pdb=" C3 LBN A 504 " pdb=" O7 LBN A 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 947 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 507 " -0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN B 507 " 0.234 2.00e-02 2.50e+03 pdb=" C5 LBN B 507 " 0.225 2.00e-02 2.50e+03 pdb=" C8 LBN B 507 " -0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 504 " 0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN A 504 " -0.234 2.00e-02 2.50e+03 pdb=" C5 LBN A 504 " -0.225 2.00e-02 2.50e+03 pdb=" C8 LBN A 504 " 0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C TYR A 238 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 50 2.59 - 3.17: 5211 3.17 - 3.74: 8818 3.74 - 4.32: 11582 4.32 - 4.90: 20322 Nonbonded interactions: 45983 Sorted by model distance: nonbonded pdb=" OD1 ASP A 132 " pdb="MG MG A 501 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASP B 132 " pdb="MG MG B 504 " model vdw 2.011 2.170 nonbonded pdb="MG MG B 505 " pdb=" O1A CDP B 516 " model vdw 2.024 2.170 nonbonded pdb="MG MG A 502 " pdb=" O1A CDP A 513 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A 136 " pdb="MG MG A 501 " model vdw 2.060 2.170 ... (remaining 45978 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 383 or resid 503 or (resid 506 and (name C10 or \ name C13 or name C16 or name C29 or name C30 or name C31 or name C32 or name C3 \ 3 or name C4 or name C7 )) or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 509 or (re \ sid 510 and (name C10 or name C13 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) or re \ sid 511 or (resid 512 and (name C25 or name C26 or name C27 or name C28 or name \ C29 or name C30 or name C31 or name C32)) or resid 514 or (resid 515 and (name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or na \ me C32)))) selection = (chain 'B' and (resid 20 through 383 or (resid 503 and (name C10 or name C13 or \ name C16 or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 \ or name C7 )) or resid 506 or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 511 or (re \ sid 512 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32)) or (resid 514 and (name C10 or name C13 or name C26 \ or name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name \ C33 or name C4 or name C7 )) or (resid 515 and (name C25 or name C26 or name C27 \ or name C28 or name C29 or name C30 or name C31 or name C32)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 6274 Z= 0.318 Angle : 0.863 15.587 8416 Z= 0.404 Chirality : 0.044 0.258 950 Planarity : 0.012 0.229 972 Dihedral : 19.471 131.617 2402 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 0.41 (0.32), residues: 724 helix: 1.78 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 120 TYR 0.011 0.001 TYR A 282 PHE 0.015 0.002 PHE A 165 TRP 0.020 0.001 TRP A 176 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.32 ( 6274) covalent geometry : angle 0.86273 / 0.40 ( 8416) hydrogen bonds : bond 0.13218 / 8.12 ( 406) hydrogen bonds : angle 5.57681 / 3.95 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.210 Fit side-chains REVERT: A 60 TRP cc_start: 0.8512 (p-90) cc_final: 0.8231 (p-90) REVERT: A 159 TRP cc_start: 0.8535 (m100) cc_final: 0.8180 (m100) REVERT: A 193 GLU cc_start: 0.7346 (mp0) cc_final: 0.6891 (mp0) REVERT: A 201 MET cc_start: 0.6745 (ttp) cc_final: 0.6442 (ttp) REVERT: A 262 THR cc_start: 0.7762 (t) cc_final: 0.7363 (p) REVERT: A 292 GLN cc_start: 0.7658 (tt0) cc_final: 0.7454 (tt0) REVERT: A 317 MET cc_start: 0.6932 (mtp) cc_final: 0.6531 (mtp) REVERT: B 25 GLN cc_start: 0.7781 (tt0) cc_final: 0.7454 (tt0) REVERT: B 60 TRP cc_start: 0.8508 (p-90) cc_final: 0.8230 (p-90) REVERT: B 159 TRP cc_start: 0.8537 (m100) cc_final: 0.8179 (m100) REVERT: B 193 GLU cc_start: 0.7349 (mp0) cc_final: 0.6891 (mp0) REVERT: B 201 MET cc_start: 0.6755 (ttp) cc_final: 0.6454 (ttp) REVERT: B 262 THR cc_start: 0.7762 (t) cc_final: 0.7366 (p) REVERT: B 292 GLN cc_start: 0.7653 (tt0) cc_final: 0.7449 (tt0) REVERT: B 317 MET cc_start: 0.6935 (mtp) cc_final: 0.6534 (mtp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0721 time to fit residues: 10.2444 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 242 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.202436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161820 restraints weight = 6374.655| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.71 r_work: 0.3718 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6274 Z= 0.178 Angle : 0.652 5.895 8416 Z= 0.347 Chirality : 0.043 0.161 950 Planarity : 0.005 0.043 972 Dihedral : 17.939 127.673 1144 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.27 % Allowed : 9.21 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.32), residues: 724 helix: 1.94 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.74 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 120 TYR 0.016 0.002 TYR A 297 PHE 0.024 0.002 PHE A 301 TRP 0.022 0.002 TRP A 176 HIS 0.005 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 ( 6274) covalent geometry : angle 0.65210 / 0.35 ( 8416) hydrogen bonds : bond 0.07672 / 5.04 ( 406) hydrogen bonds : angle 4.19347 / 2.95 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.257 Fit side-chains REVERT: A 60 TRP cc_start: 0.8595 (p-90) cc_final: 0.8244 (p-90) REVERT: A 130 MET cc_start: 0.6365 (mtt) cc_final: 0.6020 (mtt) REVERT: A 188 ILE cc_start: 0.7658 (pt) cc_final: 0.7440 (pt) REVERT: A 201 MET cc_start: 0.7689 (ttp) cc_final: 0.7432 (mtp) REVERT: A 317 MET cc_start: 0.7156 (mtp) cc_final: 0.6905 (mtp) REVERT: B 60 TRP cc_start: 0.8596 (p-90) cc_final: 0.8248 (p-90) REVERT: B 130 MET cc_start: 0.6360 (mtt) cc_final: 0.6012 (mtt) REVERT: B 188 ILE cc_start: 0.7643 (pt) cc_final: 0.7428 (pt) REVERT: B 201 MET cc_start: 0.7676 (ttp) cc_final: 0.7417 (mtp) REVERT: B 317 MET cc_start: 0.7107 (mtp) cc_final: 0.6841 (mtp) REVERT: B 355 MET cc_start: 0.7840 (ttp) cc_final: 0.7639 (ttp) outliers start: 8 outliers final: 8 residues processed: 79 average time/residue: 0.0656 time to fit residues: 7.3907 Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.206787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166861 restraints weight = 6345.657| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.72 r_work: 0.3774 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6274 Z= 0.141 Angle : 0.578 6.200 8416 Z= 0.310 Chirality : 0.040 0.135 950 Planarity : 0.004 0.043 972 Dihedral : 15.213 118.710 1144 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.75 % Allowed : 10.95 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.32), residues: 724 helix: 2.25 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.012 0.001 TYR A 297 PHE 0.014 0.001 PHE A 301 TRP 0.013 0.001 TRP A 52 HIS 0.005 0.002 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 6274) covalent geometry : angle 0.57792 / 0.31 ( 8416) hydrogen bonds : bond 0.06377 / 4.18 ( 406) hydrogen bonds : angle 3.95607 / 2.77 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.206 Fit side-chains REVERT: A 60 TRP cc_start: 0.8613 (p-90) cc_final: 0.8311 (p-90) REVERT: A 130 MET cc_start: 0.6491 (mtt) cc_final: 0.5995 (mtt) REVERT: A 152 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7700 (mtm180) REVERT: A 317 MET cc_start: 0.7041 (mtp) cc_final: 0.6798 (mtp) REVERT: B 60 TRP cc_start: 0.8619 (p-90) cc_final: 0.8321 (p-90) REVERT: B 130 MET cc_start: 0.6490 (mtt) cc_final: 0.5979 (mtt) REVERT: B 152 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7713 (mtm180) REVERT: B 317 MET cc_start: 0.7152 (mtp) cc_final: 0.6932 (mtp) REVERT: B 355 MET cc_start: 0.7655 (ttp) cc_final: 0.7420 (ttp) outliers start: 11 outliers final: 3 residues processed: 81 average time/residue: 0.0810 time to fit residues: 8.7170 Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 175 GLN A 372 GLN B 175 GLN B 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.205833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165717 restraints weight = 6333.099| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.72 r_work: 0.3757 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6274 Z= 0.139 Angle : 0.559 6.137 8416 Z= 0.301 Chirality : 0.039 0.145 950 Planarity : 0.004 0.044 972 Dihedral : 14.210 115.156 1144 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.06 % Allowed : 12.54 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.32), residues: 724 helix: 2.23 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -2.68 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 120 TYR 0.014 0.001 TYR B 49 PHE 0.016 0.001 PHE B 165 TRP 0.017 0.001 TRP A 52 HIS 0.005 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 6274) covalent geometry : angle 0.55850 / 0.30 ( 8416) hydrogen bonds : bond 0.06318 / 4.16 ( 406) hydrogen bonds : angle 3.89088 / 2.73 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.209 Fit side-chains REVERT: A 60 TRP cc_start: 0.8622 (p-90) cc_final: 0.8357 (p-90) REVERT: A 130 MET cc_start: 0.6495 (mtt) cc_final: 0.5938 (mtt) REVERT: A 152 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7750 (mtm180) REVERT: A 185 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7014 (mtpt) REVERT: A 317 MET cc_start: 0.6967 (mtp) cc_final: 0.6738 (mtp) REVERT: B 60 TRP cc_start: 0.8622 (p-90) cc_final: 0.8357 (p-90) REVERT: B 130 MET cc_start: 0.6627 (mtt) cc_final: 0.6068 (mtt) REVERT: B 152 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7779 (mtm180) REVERT: B 317 MET cc_start: 0.7085 (mtp) cc_final: 0.6873 (mtp) REVERT: B 355 MET cc_start: 0.7644 (ttp) cc_final: 0.7395 (ttp) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.0734 time to fit residues: 8.2861 Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.0670 chunk 10 optimal weight: 0.1980 chunk 55 optimal weight: 0.0030 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170942 restraints weight = 6516.719| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.74 r_work: 0.3820 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6274 Z= 0.128 Angle : 0.539 6.146 8416 Z= 0.293 Chirality : 0.038 0.135 950 Planarity : 0.004 0.043 972 Dihedral : 13.206 110.671 1144 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.27 % Allowed : 14.92 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.32), residues: 724 helix: 2.40 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -2.62 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.018 0.001 TYR A 49 PHE 0.014 0.001 PHE A 165 TRP 0.016 0.001 TRP A 52 HIS 0.005 0.002 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 ( 6274) covalent geometry : angle 0.53856 / 0.29 ( 8416) hydrogen bonds : bond 0.05600 / 3.67 ( 406) hydrogen bonds : angle 3.77573 / 2.66 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.213 Fit side-chains REVERT: A 28 LYS cc_start: 0.5562 (mttt) cc_final: 0.5132 (tptm) REVERT: A 60 TRP cc_start: 0.8662 (p-90) cc_final: 0.8404 (p-90) REVERT: A 130 MET cc_start: 0.6315 (mtt) cc_final: 0.5836 (mtt) REVERT: A 317 MET cc_start: 0.7080 (mtp) cc_final: 0.6867 (mtp) REVERT: B 60 TRP cc_start: 0.8660 (p-90) cc_final: 0.8402 (p-90) REVERT: B 130 MET cc_start: 0.6456 (mtt) cc_final: 0.5971 (mtt) REVERT: B 317 MET cc_start: 0.7064 (mtp) cc_final: 0.6854 (mtp) REVERT: B 355 MET cc_start: 0.7599 (ttp) cc_final: 0.7349 (ttp) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.0678 time to fit residues: 7.2549 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161073 restraints weight = 6348.227| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.74 r_work: 0.3716 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6274 Z= 0.156 Angle : 0.588 6.123 8416 Z= 0.316 Chirality : 0.040 0.159 950 Planarity : 0.004 0.044 972 Dihedral : 13.037 104.027 1144 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.27 % Allowed : 15.71 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.32), residues: 724 helix: 2.41 (0.22), residues: 488 sheet: None (None), residues: 0 loop : -2.57 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.018 0.002 TYR A 49 PHE 0.019 0.002 PHE A 301 TRP 0.019 0.001 TRP A 52 HIS 0.005 0.002 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 6274) covalent geometry : angle 0.58783 / 0.32 ( 8416) hydrogen bonds : bond 0.06928 / 4.56 ( 406) hydrogen bonds : angle 3.91158 / 2.75 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.222 Fit side-chains REVERT: A 28 LYS cc_start: 0.5666 (mttt) cc_final: 0.5187 (tptm) REVERT: A 60 TRP cc_start: 0.8675 (p-90) cc_final: 0.8347 (p-90) REVERT: A 130 MET cc_start: 0.6606 (mtt) cc_final: 0.6066 (mtt) REVERT: A 177 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 317 MET cc_start: 0.7283 (mtp) cc_final: 0.7066 (mtp) REVERT: B 60 TRP cc_start: 0.8669 (p-90) cc_final: 0.8342 (p-90) REVERT: B 130 MET cc_start: 0.6589 (mtt) cc_final: 0.6042 (mtt) REVERT: B 317 MET cc_start: 0.7276 (mtp) cc_final: 0.7063 (mtp) REVERT: B 355 MET cc_start: 0.7764 (ttp) cc_final: 0.7466 (ttp) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0788 time to fit residues: 7.9341 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.204230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163681 restraints weight = 6358.865| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.73 r_work: 0.3739 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6274 Z= 0.141 Angle : 0.563 6.138 8416 Z= 0.304 Chirality : 0.039 0.143 950 Planarity : 0.004 0.044 972 Dihedral : 12.673 100.506 1144 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.43 % Allowed : 16.83 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.32), residues: 724 helix: 2.41 (0.22), residues: 488 sheet: None (None), residues: 0 loop : -2.57 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.021 0.001 TYR B 49 PHE 0.016 0.002 PHE B 165 TRP 0.024 0.001 TRP A 52 HIS 0.005 0.002 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 6274) covalent geometry : angle 0.56317 / 0.30 ( 8416) hydrogen bonds : bond 0.06407 / 4.22 ( 406) hydrogen bonds : angle 3.85215 / 2.71 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.247 Fit side-chains REVERT: A 28 LYS cc_start: 0.5516 (mttt) cc_final: 0.5045 (tptm) REVERT: A 60 TRP cc_start: 0.8699 (p-90) cc_final: 0.8374 (p-90) REVERT: A 130 MET cc_start: 0.6536 (mtt) cc_final: 0.6029 (mtt) REVERT: A 177 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 60 TRP cc_start: 0.8696 (p-90) cc_final: 0.8373 (p-90) REVERT: B 130 MET cc_start: 0.6506 (mtt) cc_final: 0.5993 (mtt) REVERT: B 355 MET cc_start: 0.7744 (ttp) cc_final: 0.7440 (ttp) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.0740 time to fit residues: 7.5072 Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 280 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165049 restraints weight = 6361.788| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.73 r_work: 0.3755 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6274 Z= 0.136 Angle : 0.552 6.221 8416 Z= 0.297 Chirality : 0.038 0.136 950 Planarity : 0.004 0.044 972 Dihedral : 12.043 93.702 1144 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.90 % Allowed : 16.35 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.32), residues: 724 helix: 2.46 (0.22), residues: 488 sheet: None (None), residues: 0 loop : -2.54 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.021 0.001 TYR A 49 PHE 0.014 0.001 PHE A 165 TRP 0.028 0.001 TRP B 52 HIS 0.005 0.002 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 ( 6274) covalent geometry : angle 0.55249 / 0.30 ( 8416) hydrogen bonds : bond 0.06095 / 4.01 ( 406) hydrogen bonds : angle 3.82497 / 2.70 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.284 Fit side-chains REVERT: A 28 LYS cc_start: 0.5288 (mttt) cc_final: 0.5027 (tptm) REVERT: A 60 TRP cc_start: 0.8686 (p-90) cc_final: 0.8360 (p-90) REVERT: A 84 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7249 (t80) REVERT: A 130 MET cc_start: 0.6447 (mtt) cc_final: 0.5989 (mtt) REVERT: A 316 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.4856 (p-80) REVERT: B 60 TRP cc_start: 0.8693 (p-90) cc_final: 0.8356 (p-90) REVERT: B 84 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7263 (t80) REVERT: B 130 MET cc_start: 0.6415 (mtt) cc_final: 0.5948 (mtt) REVERT: B 316 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.4872 (p-80) REVERT: B 355 MET cc_start: 0.7669 (ttp) cc_final: 0.7364 (ttp) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.0720 time to fit residues: 7.3459 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.205290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164974 restraints weight = 6377.881| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.73 r_work: 0.3751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6274 Z= 0.136 Angle : 0.552 6.168 8416 Z= 0.298 Chirality : 0.040 0.238 950 Planarity : 0.004 0.044 972 Dihedral : 11.591 85.951 1144 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.02 % Allowed : 16.03 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.32), residues: 724 helix: 2.43 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.022 0.001 TYR A 49 PHE 0.015 0.001 PHE B 165 TRP 0.024 0.001 TRP B 52 HIS 0.005 0.002 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 ( 6274) covalent geometry : angle 0.55228 / 0.30 ( 8416) hydrogen bonds : bond 0.06107 / 4.03 ( 406) hydrogen bonds : angle 3.80174 / 2.68 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.225 Fit side-chains REVERT: A 28 LYS cc_start: 0.5283 (mttt) cc_final: 0.4994 (tptm) REVERT: A 60 TRP cc_start: 0.8684 (p-90) cc_final: 0.8363 (p-90) REVERT: A 84 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7197 (t80) REVERT: A 130 MET cc_start: 0.6508 (mtt) cc_final: 0.6075 (mtt) REVERT: A 316 HIS cc_start: 0.5876 (OUTLIER) cc_final: 0.4805 (p-80) REVERT: A 321 GLU cc_start: 0.7401 (tt0) cc_final: 0.7093 (pm20) REVERT: B 60 TRP cc_start: 0.8683 (p-90) cc_final: 0.8364 (p-90) REVERT: B 84 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 130 MET cc_start: 0.6483 (mtt) cc_final: 0.6049 (mtt) REVERT: B 152 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7441 (mtm180) REVERT: B 316 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.4840 (p-80) REVERT: B 355 MET cc_start: 0.7663 (ttp) cc_final: 0.7330 (ttp) outliers start: 19 outliers final: 10 residues processed: 76 average time/residue: 0.0736 time to fit residues: 7.8196 Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.200704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159604 restraints weight = 6384.879| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.73 r_work: 0.3700 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6274 Z= 0.158 Angle : 0.598 7.239 8416 Z= 0.322 Chirality : 0.041 0.218 950 Planarity : 0.005 0.045 972 Dihedral : 11.710 81.508 1144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.06 % Allowed : 17.30 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.32), residues: 724 helix: 2.32 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -2.53 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.022 0.002 TYR A 49 PHE 0.018 0.002 PHE B 165 TRP 0.025 0.002 TRP B 52 HIS 0.005 0.002 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 6274) covalent geometry : angle 0.59772 / 0.32 ( 8416) hydrogen bonds : bond 0.06830 / 4.50 ( 406) hydrogen bonds : angle 3.90652 / 2.75 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.224 Fit side-chains REVERT: A 60 TRP cc_start: 0.8728 (p-90) cc_final: 0.8335 (p-90) REVERT: A 130 MET cc_start: 0.6583 (mtt) cc_final: 0.6086 (mtt) REVERT: A 177 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 316 HIS cc_start: 0.6133 (OUTLIER) cc_final: 0.5070 (p-80) REVERT: B 60 TRP cc_start: 0.8730 (p-90) cc_final: 0.8339 (p-90) REVERT: B 130 MET cc_start: 0.6574 (mtt) cc_final: 0.6074 (mtt) REVERT: B 316 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5069 (p-80) REVERT: B 355 MET cc_start: 0.7754 (ttp) cc_final: 0.7423 (ttp) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.0760 time to fit residues: 7.6656 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.197964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156577 restraints weight = 6341.661| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.75 r_work: 0.3654 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6274 Z= 0.170 Angle : 0.617 6.294 8416 Z= 0.332 Chirality : 0.042 0.203 950 Planarity : 0.005 0.044 972 Dihedral : 11.964 76.570 1144 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.59 % Allowed : 17.46 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.32), residues: 724 helix: 2.22 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.024 0.002 TYR A 49 PHE 0.019 0.002 PHE B 165 TRP 0.027 0.002 TRP A 52 HIS 0.005 0.002 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 6274) covalent geometry : angle 0.61658 / 0.33 ( 8416) hydrogen bonds : bond 0.07358 / 4.86 ( 406) hydrogen bonds : angle 3.98572 / 2.80 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.84 seconds wall clock time: 25 minutes 58.49 seconds (1558.49 seconds total)