Starting phenix.real_space_refine on Thu Jul 2 07:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ubb_26437/07_2026/7ubb_26437.map" } resolution = 4.5 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= 0.026 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 24 5.16 5 C 4816 2.51 5 N 1256 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7448 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: D, E, F, G, H, I, J Time building chain proxies: 1.12, per 1000 atoms: 0.15 Number of scatterers: 7448 At special positions: 0 Unit cell: (96.193, 92.597, 151.032, 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 24 16.00 O 1352 8.00 N 1256 7.00 C 4816 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: 0.57 Conformation dependent library (CDL) restraints added in 415.9 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 40.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'C' and resid 110 through 121 removed outlier: 3.662A pdb=" N GLY C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP D 216 " --> pdb=" O MET D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.663A pdb=" N GLY E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 189 Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS E 198 " --> pdb=" O PHE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 216 removed outlier: 3.596A pdb=" N TRP E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS F 198 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP F 216 " --> pdb=" O MET F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS G 198 " --> pdb=" O PHE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 216 removed outlier: 3.596A pdb=" N TRP G 216 " --> pdb=" O MET G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 189 Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP H 216 " --> pdb=" O MET H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 189 Processing helix chain 'I' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP I 216 " --> pdb=" O MET I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 189 Processing helix chain 'J' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS J 198 " --> pdb=" O PHE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP J 216 " --> pdb=" O MET J 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 123 through 132 Processing sheet with id=AA2, first strand: chain 'C' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU C 147 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 123 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU D 147 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 132 Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU E 147 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 123 through 132 Processing sheet with id=AA8, first strand: chain 'F' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU F 147 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 123 through 132 Processing sheet with id=AB1, first strand: chain 'G' and resid 136 through 139 removed outlier: 7.168A pdb=" N GLU G 147 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 132 Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU H 147 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 123 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU I 147 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 123 through 132 Processing sheet with id=AB7, first strand: chain 'J' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU J 147 " --> pdb=" O LEU J 137 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 963 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: 0.99 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2304 1.35 - 1.46: 1883 1.46 - 1.58: 3373 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7600 Sorted by residual: bond pdb=" CA ASP G 151 " pdb=" CB ASP G 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.08e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.81e-01 bond pdb=" CA ASP J 151 " pdb=" CB ASP J 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.80e-01 bond pdb=" CA ASP H 151 " pdb=" CB ASP H 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.76e-01 bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.60e-01 ... (remaining 7595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 9707 1.39 - 2.79: 372 2.79 - 4.18: 89 4.18 - 5.57: 16 5.57 - 6.97: 16 Bond angle restraints: 10200 Sorted by residual: angle pdb=" C LEU H 150 " pdb=" N ASP H 151 " pdb=" CA ASP H 151 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C LEU F 150 " pdb=" N ASP F 151 " pdb=" CA ASP F 151 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C LEU I 150 " pdb=" N ASP I 151 " pdb=" CA ASP I 151 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LEU D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU G 150 " pdb=" N ASP G 151 " pdb=" CA ASP G 151 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 10195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.08: 3696 12.08 - 24.17: 528 24.17 - 36.25: 200 36.25 - 48.33: 40 48.33 - 60.42: 40 Dihedral angle restraints: 4504 sinusoidal: 1896 harmonic: 2608 Sorted by residual: dihedral pdb=" CA SER H 214 " pdb=" C SER H 214 " pdb=" N LYS H 215 " pdb=" CA LYS H 215 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER C 214 " pdb=" C SER C 214 " pdb=" N LYS C 215 " pdb=" CA LYS C 215 " ideal model delta harmonic sigma weight residual 180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER J 214 " pdb=" C SER J 214 " pdb=" N LYS J 215 " pdb=" CA LYS J 215 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 589 0.030 - 0.060: 301 0.060 - 0.091: 144 0.091 - 0.121: 38 0.121 - 0.151: 8 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ASP I 151 " pdb=" N ASP I 151 " pdb=" C ASP I 151 " pdb=" CB ASP I 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP D 151 " pdb=" N ASP D 151 " pdb=" C ASP D 151 " pdb=" CB ASP D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP H 151 " pdb=" N ASP H 151 " pdb=" C ASP H 151 " pdb=" CB ASP H 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1077 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.010 2.00e-02 2.50e+03 1.00e-02 2.52e+00 pdb=" CG TRP F 216 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 216 " 0.010 2.00e-02 2.50e+03 9.93e-03 2.46e+00 pdb=" CG TRP I 216 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP I 216 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 216 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 216 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP I 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 216 " 0.010 2.00e-02 2.50e+03 9.91e-03 2.46e+00 pdb=" CG TRP G 216 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP G 216 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 216 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 216 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 216 " -0.001 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1212 2.77 - 3.30: 7163 3.30 - 3.83: 11913 3.83 - 4.37: 12490 4.37 - 4.90: 21741 Nonbonded interactions: 54519 Sorted by model distance: nonbonded pdb=" ND2 ASN C 127 " pdb=" OE2 GLU D 144 " model vdw 2.231 3.120 nonbonded pdb=" ND2 ASN H 127 " pdb=" OE2 GLU I 144 " model vdw 2.275 3.120 nonbonded pdb=" O LYS F 186 " pdb=" OG SER F 190 " model vdw 2.299 3.040 nonbonded pdb=" O LYS E 186 " pdb=" OG SER E 190 " model vdw 2.299 3.040 nonbonded pdb=" O LYS J 186 " pdb=" OG SER J 190 " model vdw 2.299 3.040 ... (remaining 54514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.130 Find NCS groups from input model: 0.080 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 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 : 0.002 0.022 7600 Z= 0.122 Angle : 0.684 6.967 10200 Z= 0.355 Chirality : 0.043 0.151 1080 Planarity : 0.002 0.010 1248 Dihedral : 14.316 60.416 2840 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -1.04 (0.26), residues: 880 helix: 1.14 (0.29), residues: 280 sheet: 0.11 (0.33), residues: 272 loop : -3.15 (0.23), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 132 TYR 0.008 0.001 TYR I 110 PHE 0.004 0.001 PHE C 194 TRP 0.026 0.002 TRP F 216 HIS 0.001 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 7600) covalent geometry : angle 0.68431 / 0.36 (10200) hydrogen bonds : bond 0.07258 / 4.87 ( 321) hydrogen bonds : angle 4.61324 / 3.12 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 Fit side-chains REVERT: C 135 GLU cc_start: 0.8466 (tp30) cc_final: 0.5309 (mt-10) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0908 time to fit residues: 1.8569 Evaluate side-chains 9 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 122 GLN C 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.222717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.182888 restraints weight = 1235.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.189006 restraints weight = 782.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.193632 restraints weight = 554.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.197370 restraints weight = 420.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200433 restraints weight = 333.077| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7600 Z= 0.096 Angle : 0.536 5.917 10200 Z= 0.286 Chirality : 0.044 0.150 1080 Planarity : 0.002 0.010 1248 Dihedral : 3.657 12.714 984 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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: -1.00 (0.27), residues: 880 helix: 1.07 (0.30), residues: 288 sheet: 0.22 (0.33), residues: 272 loop : -3.22 (0.23), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.004 0.001 TYR I 110 PHE 0.004 0.001 PHE I 194 TRP 0.012 0.001 TRP E 216 HIS 0.001 0.001 HIS J 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 ( 7600) covalent geometry : angle 0.53553 / 0.29 (10200) hydrogen bonds : bond 0.02869 / 1.86 ( 321) hydrogen bonds : angle 3.95640 / 2.67 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 124 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8387 (tptt) REVERT: G 143 THR cc_start: 0.9495 (p) cc_final: 0.9267 (p) REVERT: G 148 LEU cc_start: 0.5913 (tt) cc_final: 0.5400 (tt) REVERT: G 180 LYS cc_start: 0.9269 (tttt) cc_final: 0.9039 (mmtp) REVERT: G 203 MET cc_start: 0.7897 (ptp) cc_final: 0.6871 (pmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0916 time to fit residues: 4.1559 Evaluate side-chains 25 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.0000 chunk 48 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.0000 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 38 optimal weight: 0.0050 chunk 45 optimal weight: 0.0980 overall best weight: 0.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.210085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175175 restraints weight = 1449.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181175 restraints weight = 870.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185012 restraints weight = 595.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188622 restraints weight = 444.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.190801 restraints weight = 347.166| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7600 Z= 0.122 Angle : 0.603 5.939 10200 Z= 0.324 Chirality : 0.045 0.156 1080 Planarity : 0.004 0.043 1248 Dihedral : 4.210 16.595 984 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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: -1.47 (0.26), residues: 880 helix: 0.35 (0.29), residues: 296 sheet: -0.08 (0.29), residues: 272 loop : -3.16 (0.26), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 132 TYR 0.007 0.001 TYR G 161 PHE 0.018 0.002 PHE J 194 TRP 0.020 0.002 TRP E 216 HIS 0.001 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 7600) covalent geometry : angle 0.60322 / 0.32 (10200) hydrogen bonds : bond 0.03347 / 2.16 ( 321) hydrogen bonds : angle 4.77886 / 3.26 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 124 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8238 (tptt) REVERT: G 143 THR cc_start: 0.9514 (p) cc_final: 0.9261 (p) REVERT: G 203 MET cc_start: 0.7665 (ptp) cc_final: 0.6800 (pmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0938 time to fit residues: 3.2695 Evaluate side-chains 26 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.0020 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.222547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.181649 restraints weight = 1423.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189233 restraints weight = 887.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.194554 restraints weight = 609.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.198777 restraints weight = 450.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.201073 restraints weight = 350.177| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7600 Z= 0.119 Angle : 0.622 6.000 10200 Z= 0.330 Chirality : 0.044 0.144 1080 Planarity : 0.010 0.118 1248 Dihedral : 4.737 16.017 984 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.45 (0.26), residues: 880 helix: 0.90 (0.30), residues: 288 sheet: -0.85 (0.27), residues: 296 loop : -2.94 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 132 TYR 0.006 0.001 TYR F 161 PHE 0.016 0.002 PHE D 194 TRP 0.004 0.001 TRP F 139 HIS 0.001 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7600) covalent geometry : angle 0.62225 / 0.33 (10200) hydrogen bonds : bond 0.02973 / 1.88 ( 321) hydrogen bonds : angle 5.18325 / 3.55 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 124 LYS cc_start: 0.8618 (tmtt) cc_final: 0.7890 (tptm) REVERT: G 140 ASN cc_start: 0.8596 (t0) cc_final: 0.8314 (t0) REVERT: G 143 THR cc_start: 0.9495 (p) cc_final: 0.9246 (p) REVERT: G 183 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8971 (mm-30) REVERT: G 186 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8546 (ptpp) REVERT: G 203 MET cc_start: 0.7659 (ptp) cc_final: 0.6768 (pmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0736 time to fit residues: 2.6114 Evaluate side-chains 28 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 0.4980 chunk 21 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 16 optimal weight: 0.0470 overall best weight: 0.1428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.192312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147023 restraints weight = 1510.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154183 restraints weight = 942.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.159438 restraints weight = 650.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.163584 restraints weight = 486.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.166211 restraints weight = 384.240| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7600 Z= 0.116 Angle : 0.618 5.789 10200 Z= 0.324 Chirality : 0.046 0.155 1080 Planarity : 0.006 0.071 1248 Dihedral : 4.273 12.813 984 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.61 (0.27), residues: 880 helix: 1.06 (0.31), residues: 280 sheet: -1.08 (0.27), residues: 304 loop : -3.14 (0.29), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 132 TYR 0.008 0.001 TYR G 164 PHE 0.017 0.002 PHE G 194 TRP 0.008 0.001 TRP I 139 HIS 0.000 0.000 HIS I 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 7600) covalent geometry : angle 0.61820 / 0.32 (10200) hydrogen bonds : bond 0.02915 / 1.81 ( 321) hydrogen bonds : angle 5.10722 / 3.49 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: F 152 ASN cc_start: 0.8672 (t0) cc_final: 0.8043 (m-40) REVERT: F 171 PHE cc_start: 0.8793 (t80) cc_final: 0.8562 (t80) REVERT: F 179 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7470 (mtt180) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0794 time to fit residues: 3.2186 Evaluate side-chains 29 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 0.0030 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 115 GLN F 153 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.189647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146887 restraints weight = 1335.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.152901 restraints weight = 828.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157307 restraints weight = 559.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.160822 restraints weight = 413.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.162978 restraints weight = 325.717| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7600 Z= 0.116 Angle : 0.655 5.789 10200 Z= 0.341 Chirality : 0.046 0.146 1080 Planarity : 0.002 0.015 1248 Dihedral : 3.963 12.295 984 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.01 % Allowed : 4.04 % Favored : 94.95 % 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: -1.59 (0.26), residues: 880 helix: 0.93 (0.30), residues: 288 sheet: -0.98 (0.26), residues: 304 loop : -3.18 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 141 TYR 0.012 0.001 TYR H 110 PHE 0.014 0.001 PHE I 194 TRP 0.032 0.002 TRP E 216 HIS 0.000 0.000 HIS J 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7600) covalent geometry : angle 0.65452 / 0.34 (10200) hydrogen bonds : bond 0.03517 / 2.25 ( 321) hydrogen bonds : angle 4.92346 / 3.36 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 152 ASN cc_start: 0.8742 (t0) cc_final: 0.8357 (m-40) REVERT: F 179 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7495 (mtt180) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.0627 time to fit residues: 2.4495 Evaluate side-chains 28 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 28 optimal weight: 0.0670 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 25 optimal weight: 0.0470 overall best weight: 0.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.190220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.146670 restraints weight = 1541.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153651 restraints weight = 941.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.159338 restraints weight = 635.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.163197 restraints weight = 457.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.166005 restraints weight = 353.787| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7600 Z= 0.119 Angle : 0.652 5.831 10200 Z= 0.341 Chirality : 0.045 0.148 1080 Planarity : 0.004 0.039 1248 Dihedral : 4.093 14.158 984 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.27), residues: 880 helix: 1.07 (0.31), residues: 288 sheet: -0.92 (0.27), residues: 304 loop : -3.21 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 141 TYR 0.010 0.001 TYR I 110 PHE 0.013 0.001 PHE G 194 TRP 0.019 0.002 TRP E 216 HIS 0.000 0.000 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7600) covalent geometry : angle 0.65156 / 0.34 (10200) hydrogen bonds : bond 0.03587 / 2.22 ( 321) hydrogen bonds : angle 4.75865 / 3.23 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: F 152 ASN cc_start: 0.8611 (t0) cc_final: 0.8137 (m-40) REVERT: F 179 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7466 (mtt180) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0723 time to fit residues: 2.6548 Evaluate side-chains 26 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 122 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.190892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148523 restraints weight = 1492.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156070 restraints weight = 895.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.161702 restraints weight = 595.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166243 restraints weight = 428.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.169308 restraints weight = 323.524| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7600 Z= 0.102 Angle : 0.592 5.762 10200 Z= 0.311 Chirality : 0.044 0.142 1080 Planarity : 0.002 0.010 1248 Dihedral : 3.975 15.919 984 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -1.57 (0.27), residues: 880 helix: 1.04 (0.31), residues: 288 sheet: -1.03 (0.28), residues: 304 loop : -3.19 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 141 TYR 0.009 0.001 TYR I 110 PHE 0.012 0.001 PHE D 194 TRP 0.018 0.001 TRP E 216 HIS 0.001 0.000 HIS J 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 7600) covalent geometry : angle 0.59213 / 0.31 (10200) hydrogen bonds : bond 0.03372 / 2.09 ( 321) hydrogen bonds : angle 4.64539 / 3.16 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 136 LEU cc_start: 0.7858 (pp) cc_final: 0.7344 (mp) REVERT: F 137 LEU cc_start: 0.8406 (mt) cc_final: 0.8118 (mt) REVERT: F 152 ASN cc_start: 0.8351 (t0) cc_final: 0.8036 (m-40) REVERT: F 179 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7471 (mtt180) REVERT: F 203 MET cc_start: 0.7373 (pmm) cc_final: 0.7162 (pmm) REVERT: F 215 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7999 (tmtt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0607 time to fit residues: 2.1267 Evaluate side-chains 27 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.0370 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 153 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.207340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.144827 restraints weight = 1147.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.150659 restraints weight = 818.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.155619 restraints weight = 632.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.159580 restraints weight = 514.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.162978 restraints weight = 433.531| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7600 Z= 0.116 Angle : 0.614 5.825 10200 Z= 0.323 Chirality : 0.044 0.145 1080 Planarity : 0.002 0.010 1248 Dihedral : 4.128 14.653 984 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.25), residues: 880 helix: 0.91 (0.29), residues: 288 sheet: -1.27 (0.31), residues: 224 loop : -2.90 (0.24), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 141 TYR 0.008 0.001 TYR G 110 PHE 0.012 0.001 PHE C 194 TRP 0.026 0.002 TRP F 216 HIS 0.001 0.001 HIS J 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7600) covalent geometry : angle 0.61423 / 0.32 (10200) hydrogen bonds : bond 0.03783 / 2.33 ( 321) hydrogen bonds : angle 4.91223 / 3.36 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.8521 (m-80) cc_final: 0.7852 (m-80) REVERT: E 150 LEU cc_start: 0.6014 (pp) cc_final: 0.5722 (pt) REVERT: E 162 CYS cc_start: 0.9377 (t) cc_final: 0.9083 (p) REVERT: E 171 PHE cc_start: 0.8143 (t80) cc_final: 0.7202 (m-10) REVERT: E 218 ILE cc_start: 0.5920 (tt) cc_final: 0.5669 (tt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0806 time to fit residues: 4.0307 Evaluate side-chains 40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 85 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 153 ASN E 166 GLN E 185 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.197928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.134889 restraints weight = 1271.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.139297 restraints weight = 1012.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.143276 restraints weight = 846.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.146131 restraints weight = 729.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148089 restraints weight = 645.829| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7600 Z= 0.125 Angle : 0.775 9.309 10200 Z= 0.412 Chirality : 0.049 0.153 1080 Planarity : 0.004 0.033 1248 Dihedral : 4.932 20.355 984 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.02 % Allowed : 0.00 % Favored : 97.98 % 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: -2.13 (0.25), residues: 880 helix: 0.52 (0.28), residues: 288 sheet: -1.33 (0.31), residues: 224 loop : -3.10 (0.24), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG F 119 TYR 0.008 0.001 TYR C 161 PHE 0.009 0.001 PHE F 194 TRP 0.042 0.004 TRP H 196 HIS 0.002 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 7600) covalent geometry : angle 0.77467 / 0.41 (10200) hydrogen bonds : bond 0.04082 / 2.55 ( 321) hydrogen bonds : angle 4.78767 / 3.27 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: E 113 TYR cc_start: 0.8542 (m-80) cc_final: 0.7851 (m-80) REVERT: E 136 LEU cc_start: 0.8624 (pp) cc_final: 0.8387 (pp) REVERT: E 162 CYS cc_start: 0.9438 (t) cc_final: 0.9171 (p) REVERT: E 171 PHE cc_start: 0.8161 (t80) cc_final: 0.6918 (m-10) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.0641 time to fit residues: 2.7091 Evaluate side-chains 34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 153 ASN E 166 GLN E 185 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.200710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.140882 restraints weight = 1262.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.146261 restraints weight = 947.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.150518 restraints weight = 762.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.154871 restraints weight = 638.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.157252 restraints weight = 549.312| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7600 Z= 0.129 Angle : 0.785 8.618 10200 Z= 0.432 Chirality : 0.048 0.146 1080 Planarity : 0.004 0.032 1248 Dihedral : 5.039 18.144 984 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.02 % Allowed : 1.01 % Favored : 96.97 % 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: -2.37 (0.24), residues: 880 helix: 0.23 (0.28), residues: 296 sheet: -1.77 (0.29), residues: 224 loop : -2.98 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG C 132 TYR 0.007 0.001 TYR H 176 PHE 0.011 0.002 PHE F 194 TRP 0.020 0.002 TRP D 216 HIS 0.001 0.001 HIS E 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 7600) covalent geometry : angle 0.78492 / 0.43 (10200) hydrogen bonds : bond 0.04304 / 2.68 ( 321) hydrogen bonds : angle 5.29349 / 3.58 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.81 seconds wall clock time: 17 minutes 51.46 seconds (1071.46 seconds total)