Starting phenix.real_space_refine on Tue Feb 3 14:05:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.map" model { file = "/net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdm_44462/02_2026/9bdm_44462.cif" } resolution = 3.63 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= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2290 2.51 5 N 580 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3535 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.54, per 1000 atoms: 0.15 Number of scatterers: 3535 At special positions: 0 Unit cell: (72.842, 82.302, 40.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 660 8.00 N 580 7.00 C 2290 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: 0.16 Conformation dependent library (CDL) restraints added in 80.0 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.615A pdb=" N LEU B 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS D 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20 removed outlier: 6.410A pdb=" N ALA A 19 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 19 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 34 removed outlier: 6.282A pdb=" N ASN A 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL C 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN C 27 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL E 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA C 29 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL E 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 34 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 33 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 64 removed outlier: 9.075A pdb=" N THR B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N GLU D 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU B 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR C 60 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 61 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU C 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR E 60 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU C 61 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU E 62 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 70 through 73 removed outlier: 7.015A pdb=" N LYS B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE D 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU B 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 78 through 80 removed outlier: 6.956A pdb=" N LYS D 80 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99 removed outlier: 6.528A pdb=" N GLU B 92 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE D 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 94 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR B 96 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASP D 99 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN B 98 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR C 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN C 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 108 removed outlier: 6.796A pdb=" N ARG B 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE D 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR B 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 121 removed outlier: 5.879A pdb=" N SER B 115 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR D 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER B 117 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA D 120 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 119 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A 115 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR B 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER A 117 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ALA B 120 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A 119 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 115 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER E 115 " --> pdb=" O TYR C 114 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 0.29 Time building geometry restraints manager: 0.23 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: 1100 1.34 - 1.46: 782 1.46 - 1.57: 1728 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 3620 Sorted by residual: bond pdb=" CA ASN E 27 " pdb=" CB ASN E 27 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.50e-02 4.44e+03 5.85e-01 bond pdb=" CA ASN A 27 " pdb=" CB ASN A 27 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.50e-02 4.44e+03 5.27e-01 bond pdb=" CA ASN D 27 " pdb=" CB ASN D 27 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.50e-02 4.44e+03 4.98e-01 bond pdb=" CA ASN C 27 " pdb=" CB ASN C 27 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.50e-02 4.44e+03 4.96e-01 bond pdb=" CA ASN B 27 " pdb=" CB ASN B 27 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.50e-02 4.44e+03 4.64e-01 ... (remaining 3615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 4667 1.13 - 2.25: 211 2.25 - 3.38: 42 3.38 - 4.50: 0 4.50 - 5.63: 5 Bond angle restraints: 4925 Sorted by residual: angle pdb=" N ASN A 27 " pdb=" CA ASN A 27 " pdb=" C ASN A 27 " ideal model delta sigma weight residual 108.41 102.78 5.63 1.63e+00 3.76e-01 1.19e+01 angle pdb=" N ASN E 27 " pdb=" CA ASN E 27 " pdb=" C ASN E 27 " ideal model delta sigma weight residual 108.41 102.78 5.63 1.63e+00 3.76e-01 1.19e+01 angle pdb=" N ASN B 27 " pdb=" CA ASN B 27 " pdb=" C ASN B 27 " ideal model delta sigma weight residual 108.41 102.82 5.59 1.63e+00 3.76e-01 1.18e+01 angle pdb=" N ASN D 27 " pdb=" CA ASN D 27 " pdb=" C ASN D 27 " ideal model delta sigma weight residual 108.41 102.86 5.55 1.63e+00 3.76e-01 1.16e+01 angle pdb=" N ASN C 27 " pdb=" CA ASN C 27 " pdb=" C ASN C 27 " ideal model delta sigma weight residual 108.41 102.86 5.55 1.63e+00 3.76e-01 1.16e+01 ... (remaining 4920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.05: 1790 9.05 - 18.11: 225 18.11 - 27.16: 85 27.16 - 36.22: 20 36.22 - 45.27: 20 Dihedral angle restraints: 2140 sinusoidal: 815 harmonic: 1325 Sorted by residual: dihedral pdb=" CG LYS B 35 " pdb=" CD LYS B 35 " pdb=" CE LYS B 35 " pdb=" NZ LYS B 35 " ideal model delta sinusoidal sigma weight residual -180.00 -137.16 -42.84 3 1.50e+01 4.44e-03 7.69e+00 dihedral pdb=" CG LYS C 35 " pdb=" CD LYS C 35 " pdb=" CE LYS C 35 " pdb=" NZ LYS C 35 " ideal model delta sinusoidal sigma weight residual -180.00 -137.17 -42.83 3 1.50e+01 4.44e-03 7.69e+00 dihedral pdb=" CG LYS A 35 " pdb=" CD LYS A 35 " pdb=" CE LYS A 35 " pdb=" NZ LYS A 35 " ideal model delta sinusoidal sigma weight residual 180.00 -137.18 -42.82 3 1.50e+01 4.44e-03 7.69e+00 ... (remaining 2137 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.031: 322 0.031 - 0.062: 161 0.062 - 0.093: 20 0.093 - 0.124: 68 0.124 - 0.154: 9 Chirality restraints: 580 Sorted by residual: chirality pdb=" CA ASN B 27 " pdb=" N ASN B 27 " pdb=" C ASN B 27 " pdb=" CB ASN B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASN A 27 " pdb=" N ASN A 27 " pdb=" C ASN A 27 " pdb=" CB ASN A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN E 27 " pdb=" N ASN E 27 " pdb=" C ASN E 27 " pdb=" CB ASN E 27 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 577 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 85 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO C 86 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.60e+00 pdb=" N PRO A 86 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO B 86 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " 0.033 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 528 2.78 - 3.31: 3030 3.31 - 3.84: 5972 3.84 - 4.37: 6479 4.37 - 4.90: 10758 Nonbonded interactions: 26767 Sorted by model distance: nonbonded pdb=" OG SER A 112 " pdb=" O SER C 112 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 112 " pdb=" OG SER B 112 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 112 " pdb=" OG SER D 112 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP C 74 " pdb=" NZ LYS C 76 " model vdw 2.294 3.120 nonbonded pdb=" OD1 ASP A 74 " pdb=" NZ LYS A 76 " model vdw 2.294 3.120 ... (remaining 26762 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.003 0.029 3620 Z= 0.134 Angle : 0.583 5.629 4925 Z= 0.340 Chirality : 0.050 0.154 580 Planarity : 0.006 0.059 605 Dihedral : 10.791 45.270 1280 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -2.66 (0.35), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.013 0.002 TYR C 114 PHE 0.014 0.003 PHE D 64 TRP 0.008 0.002 TRP E 79 HIS 0.002 0.000 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3620) covalent geometry : angle 0.58269 ( 4925) hydrogen bonds : bond 0.23727 ( 74) hydrogen bonds : angle 9.16060 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.079 Fit side-chains REVERT: B 13 MET cc_start: 0.7383 (ttt) cc_final: 0.6955 (ttp) REVERT: D 13 MET cc_start: 0.7547 (ttt) cc_final: 0.7129 (ttp) REVERT: E 21 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7342 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1126 time to fit residues: 2.9292 Evaluate side-chains 21 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.143265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.116067 restraints weight = 3464.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.120862 restraints weight = 1555.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.123944 restraints weight = 945.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.126118 restraints weight = 689.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.127742 restraints weight = 555.895| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3620 Z= 0.124 Angle : 0.532 6.124 4925 Z= 0.298 Chirality : 0.049 0.145 580 Planarity : 0.005 0.048 605 Dihedral : 4.707 14.353 485 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.52 % Allowed : 4.68 % Favored : 94.81 % 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: -2.63 (0.36), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.014 0.002 TYR C 114 PHE 0.019 0.002 PHE C 64 TRP 0.004 0.001 TRP E 79 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3620) covalent geometry : angle 0.53234 ( 4925) hydrogen bonds : bond 0.04007 ( 74) hydrogen bonds : angle 6.80098 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.079 Fit side-chains REVERT: B 13 MET cc_start: 0.6777 (ttt) cc_final: 0.6346 (ttp) REVERT: D 13 MET cc_start: 0.6735 (ttt) cc_final: 0.6373 (ttp) REVERT: D 74 ASP cc_start: 0.8857 (t0) cc_final: 0.8094 (m-30) REVERT: E 21 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7009 (ttp-170) REVERT: E 118 THR cc_start: 0.8277 (m) cc_final: 0.7993 (p) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1041 time to fit residues: 2.6213 Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS C 31 HIS E 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.135231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.108578 restraints weight = 3572.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.113216 restraints weight = 1619.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.116462 restraints weight = 992.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.118463 restraints weight = 717.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.119811 restraints weight = 579.280| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3620 Z= 0.184 Angle : 0.563 5.609 4925 Z= 0.317 Chirality : 0.051 0.138 580 Planarity : 0.005 0.047 605 Dihedral : 4.989 16.675 485 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.52 % Allowed : 8.05 % Favored : 91.43 % 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: -2.47 (0.37), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 21 TYR 0.018 0.003 TYR B 78 PHE 0.016 0.003 PHE C 64 TRP 0.005 0.001 TRP C 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3620) covalent geometry : angle 0.56263 ( 4925) hydrogen bonds : bond 0.04135 ( 74) hydrogen bonds : angle 5.93295 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.136 Fit side-chains REVERT: C 21 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7105 (tpp80) REVERT: D 13 MET cc_start: 0.6762 (ttt) cc_final: 0.6426 (ttp) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1563 time to fit residues: 4.2613 Evaluate side-chains 21 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS D 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.129996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.103620 restraints weight = 3721.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.108360 restraints weight = 1667.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.111428 restraints weight = 1006.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.113423 restraints weight = 726.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.114769 restraints weight = 587.438| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 3620 Z= 0.287 Angle : 0.641 6.307 4925 Z= 0.366 Chirality : 0.052 0.145 580 Planarity : 0.005 0.047 605 Dihedral : 5.424 17.958 485 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.78 % Allowed : 11.69 % Favored : 87.53 % 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: -2.46 (0.37), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 21 TYR 0.021 0.004 TYR E 78 PHE 0.021 0.004 PHE D 33 TRP 0.006 0.001 TRP C 79 HIS 0.009 0.002 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 3620) covalent geometry : angle 0.64091 ( 4925) hydrogen bonds : bond 0.04160 ( 74) hydrogen bonds : angle 5.85728 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.077 Fit side-chains REVERT: C 21 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7089 (tpp80) REVERT: D 13 MET cc_start: 0.6835 (ttt) cc_final: 0.6505 (ttp) REVERT: E 21 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7535 (ttt180) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.1126 time to fit residues: 2.8031 Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 21 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.138177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.111022 restraints weight = 3494.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.115941 restraints weight = 1514.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.119384 restraints weight = 904.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.121534 restraints weight = 640.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.122971 restraints weight = 509.531| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3620 Z= 0.096 Angle : 0.497 4.419 4925 Z= 0.275 Chirality : 0.049 0.142 580 Planarity : 0.005 0.047 605 Dihedral : 4.730 14.713 485 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.52 % Allowed : 11.95 % Favored : 87.53 % 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: -2.56 (0.37), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.012 0.002 TYR A 114 PHE 0.020 0.002 PHE C 64 TRP 0.006 0.001 TRP E 79 HIS 0.003 0.000 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3620) covalent geometry : angle 0.49662 ( 4925) hydrogen bonds : bond 0.02713 ( 74) hydrogen bonds : angle 5.71294 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.130 Fit side-chains REVERT: C 114 TYR cc_start: 0.8908 (p90) cc_final: 0.8427 (p90) REVERT: D 13 MET cc_start: 0.6730 (ttt) cc_final: 0.6412 (ttp) REVERT: E 21 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7484 (ttt180) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1330 time to fit residues: 3.3418 Evaluate side-chains 22 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.133815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107055 restraints weight = 3640.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.111878 restraints weight = 1602.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.115130 restraints weight = 963.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.117173 restraints weight = 692.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.118542 restraints weight = 557.628| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3620 Z= 0.193 Angle : 0.547 5.361 4925 Z= 0.310 Chirality : 0.050 0.136 580 Planarity : 0.005 0.044 605 Dihedral : 4.961 15.998 485 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.78 % Allowed : 12.21 % Favored : 87.01 % 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: -2.52 (0.37), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.015 0.003 TYR E 78 PHE 0.015 0.003 PHE C 64 TRP 0.005 0.001 TRP C 79 HIS 0.006 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3620) covalent geometry : angle 0.54729 ( 4925) hydrogen bonds : bond 0.03475 ( 74) hydrogen bonds : angle 5.61731 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.077 Fit side-chains REVERT: D 13 MET cc_start: 0.6770 (ttt) cc_final: 0.6496 (ttp) REVERT: D 21 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7565 (ttm-80) REVERT: E 21 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7506 (ttt180) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.1129 time to fit residues: 2.5825 Evaluate side-chains 20 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 21 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.132002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105344 restraints weight = 3748.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110105 restraints weight = 1645.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.113221 restraints weight = 989.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.115327 restraints weight = 716.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.116757 restraints weight = 574.006| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3620 Z= 0.228 Angle : 0.583 5.657 4925 Z= 0.330 Chirality : 0.051 0.141 580 Planarity : 0.005 0.045 605 Dihedral : 5.198 16.691 485 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.52 % Allowed : 12.47 % Favored : 87.01 % 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: -2.64 (0.36), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.017 0.003 TYR B 78 PHE 0.016 0.003 PHE D 33 TRP 0.005 0.001 TRP C 79 HIS 0.007 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 3620) covalent geometry : angle 0.58296 ( 4925) hydrogen bonds : bond 0.03680 ( 74) hydrogen bonds : angle 5.58265 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.127 Fit side-chains REVERT: D 13 MET cc_start: 0.6877 (ttt) cc_final: 0.6581 (ttp) REVERT: D 21 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7507 (ttm-80) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.1646 time to fit residues: 3.7718 Evaluate side-chains 20 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS ** D 31 HIS ** 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 = 0.4349 r_free = 0.4349 target = 0.138809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.111626 restraints weight = 3595.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.116538 restraints weight = 1576.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.119995 restraints weight = 942.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.122261 restraints weight = 668.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.123754 restraints weight = 529.102| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3620 Z= 0.089 Angle : 0.511 9.423 4925 Z= 0.275 Chirality : 0.049 0.140 580 Planarity : 0.004 0.047 605 Dihedral : 4.674 14.396 485 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.52 % Allowed : 12.73 % Favored : 86.75 % 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: -2.65 (0.37), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 21 TYR 0.011 0.001 TYR A 114 PHE 0.019 0.002 PHE C 64 TRP 0.005 0.001 TRP E 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3620) covalent geometry : angle 0.51120 ( 4925) hydrogen bonds : bond 0.02628 ( 74) hydrogen bonds : angle 5.62465 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.155 Fit side-chains REVERT: C 114 TYR cc_start: 0.8849 (p90) cc_final: 0.8435 (p90) REVERT: D 13 MET cc_start: 0.6774 (ttt) cc_final: 0.6476 (ttp) REVERT: E 21 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7414 (ttt180) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1209 time to fit residues: 3.1014 Evaluate side-chains 23 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 21 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS ** D 31 HIS ** 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 = 0.4247 r_free = 0.4247 target = 0.130412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.104081 restraints weight = 3744.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.108763 restraints weight = 1667.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.111957 restraints weight = 1007.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.113982 restraints weight = 725.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.115329 restraints weight = 584.506| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3620 Z= 0.270 Angle : 0.620 6.048 4925 Z= 0.353 Chirality : 0.051 0.144 580 Planarity : 0.005 0.044 605 Dihedral : 5.303 16.819 485 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.26 % Allowed : 13.51 % Favored : 86.23 % 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: -2.73 (0.36), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.019 0.004 TYR A 114 PHE 0.021 0.004 PHE B 33 TRP 0.005 0.001 TRP C 79 HIS 0.009 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 3620) covalent geometry : angle 0.61958 ( 4925) hydrogen bonds : bond 0.03888 ( 74) hydrogen bonds : angle 5.53969 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.076 Fit side-chains REVERT: D 13 MET cc_start: 0.6911 (ttt) cc_final: 0.6598 (ttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1069 time to fit residues: 2.3292 Evaluate side-chains 19 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS ** D 31 HIS ** 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 = 0.4288 r_free = 0.4288 target = 0.133553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107086 restraints weight = 3708.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.111824 restraints weight = 1633.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.115101 restraints weight = 984.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.117210 restraints weight = 703.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.118545 restraints weight = 561.705| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3620 Z= 0.166 Angle : 0.540 5.244 4925 Z= 0.304 Chirality : 0.049 0.140 580 Planarity : 0.004 0.047 605 Dihedral : 5.081 16.618 485 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.26 % Allowed : 13.51 % Favored : 86.23 % 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: -2.75 (0.36), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.016 0.003 TYR A 114 PHE 0.016 0.002 PHE C 64 TRP 0.005 0.001 TRP C 79 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3620) covalent geometry : angle 0.54014 ( 4925) hydrogen bonds : bond 0.03269 ( 74) hydrogen bonds : angle 5.54077 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.138 Fit side-chains REVERT: D 13 MET cc_start: 0.6855 (ttt) cc_final: 0.6547 (ttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1073 time to fit residues: 2.3401 Evaluate side-chains 19 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.0040 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS ** D 31 HIS ** 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 = 0.4332 r_free = 0.4332 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.110644 restraints weight = 3572.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.115503 restraints weight = 1553.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.118877 restraints weight = 928.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.121136 restraints weight = 659.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.122381 restraints weight = 524.310| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3620 Z= 0.094 Angle : 0.489 4.543 4925 Z= 0.271 Chirality : 0.049 0.138 580 Planarity : 0.004 0.046 605 Dihedral : 4.712 15.668 485 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.52 % Allowed : 12.99 % Favored : 86.49 % 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: -2.72 (0.36), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.013 0.002 TYR A 114 PHE 0.018 0.002 PHE C 64 TRP 0.004 0.001 TRP C 79 HIS 0.002 0.000 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3620) covalent geometry : angle 0.48936 ( 4925) hydrogen bonds : bond 0.02646 ( 74) hydrogen bonds : angle 5.50890 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 572.69 seconds wall clock time: 10 minutes 34.87 seconds (634.87 seconds total)