Starting phenix.real_space_refine on Tue Feb 3 23:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei5_48077/02_2026/9ei5_48077.map" } resolution = 2.84 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= -0.002 sd= 0.085 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 36 5.16 5 C 4791 2.51 5 N 1266 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 7514 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3271 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 1.56, per 1000 atoms: 0.21 Number of scatterers: 7514 At special positions: 0 Unit cell: (68.8, 104.06, 162.54, 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 36 16.00 O 1421 8.00 N 1266 7.00 C 4791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.05 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 0.69 Conformation dependent library (CDL) restraints added in 201.3 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 40.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 18 through 46 removed outlier: 4.352A pdb=" N ARG A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix removed outlier: 3.515A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 136 removed outlier: 3.961A pdb=" N GLN A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.630A pdb=" N HIS A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 166 through 169 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 193 through 1020 removed outlier: 4.113A pdb=" N LEU A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A1006 " --> pdb=" O ASP A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1042 Processing helix chain 'A' and resid 1055 through 1080 Processing helix chain 'A' and resid 1084 through 1102 Processing helix chain 'A' and resid 1102 through 288 removed outlier: 3.871A pdb=" N LEU A1106 " --> pdb=" O ILE A1102 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.615A pdb=" N GLU A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 Proline residue: A 320 - end of helix removed outlier: 4.154A pdb=" N PHE A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.006A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.975A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.887A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.630A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.501A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 177 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 8 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.887A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.854A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 195 " --> pdb=" O HIS H 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.854A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.656A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 212 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL H 221 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.839A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.585A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.648A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 93 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.648A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 87 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.720A pdb=" N PHE L 120 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 155 through 156 444 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2321 1.34 - 1.46: 1862 1.46 - 1.58: 3447 1.58 - 1.71: 0 1.71 - 1.83: 53 Bond restraints: 7683 Sorted by residual: bond pdb=" CB ASP A1073 " pdb=" CG ASP A1073 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 3.00e+00 bond pdb=" CB ARG H 101 " pdb=" CG ARG H 101 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" C THR H 179 " pdb=" N PHE H 180 " ideal model delta sigma weight residual 1.340 1.240 0.100 5.87e-02 2.90e+02 2.92e+00 bond pdb=" CB VAL H 67 " pdb=" CG1 VAL H 67 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CE1 TYR L 95 " pdb=" CZ TYR L 95 " ideal model delta sigma weight residual 1.378 1.337 0.041 2.40e-02 1.74e+03 2.85e+00 ... (remaining 7678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10154 2.36 - 4.71: 226 4.71 - 7.07: 39 7.07 - 9.43: 8 9.43 - 11.78: 1 Bond angle restraints: 10428 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" CA LEU A1048 " pdb=" CB LEU A1048 " pdb=" CG LEU A1048 " ideal model delta sigma weight residual 116.30 128.08 -11.78 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA CYS L 89 " pdb=" CB CYS L 89 " pdb=" SG CYS L 89 " ideal model delta sigma weight residual 114.40 121.59 -7.19 2.30e+00 1.89e-01 9.78e+00 angle pdb=" C VAL L 152 " pdb=" N ASP L 153 " pdb=" CA ASP L 153 " ideal model delta sigma weight residual 122.46 126.60 -4.14 1.41e+00 5.03e-01 8.62e+00 angle pdb=" N ALA H 52 " pdb=" CA ALA H 52 " pdb=" C ALA H 52 " ideal model delta sigma weight residual 108.60 112.73 -4.13 1.46e+00 4.69e-01 8.02e+00 ... (remaining 10423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4113 17.89 - 35.78: 386 35.78 - 53.67: 65 53.67 - 71.56: 12 71.56 - 89.46: 8 Dihedral angle restraints: 4584 sinusoidal: 1752 harmonic: 2832 Sorted by residual: dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual 93.00 40.11 52.89 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 134.96 -41.96 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA ASN L 139 " pdb=" C ASN L 139 " pdb=" N ASN L 140 " pdb=" CA ASN L 140 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 700 0.040 - 0.080: 331 0.080 - 0.120: 105 0.120 - 0.160: 34 0.160 - 0.201: 7 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CB VAL A 318 " pdb=" CA VAL A 318 " pdb=" CG1 VAL A 318 " pdb=" CG2 VAL A 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE H 209 " pdb=" N ILE H 209 " pdb=" C ILE H 209 " pdb=" CB ILE H 209 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA TYR L 50 " pdb=" N TYR L 50 " pdb=" C TYR L 50 " pdb=" CB TYR L 50 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 1174 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 101 " -0.341 9.50e-02 1.11e+02 1.53e-01 1.45e+01 pdb=" NE ARG H 101 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 101 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 101 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 101 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 113 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ALA H 113 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA H 113 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE H 114 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.032 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO H 109 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.027 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1136 2.76 - 3.29: 6685 3.29 - 3.83: 11923 3.83 - 4.36: 12890 4.36 - 4.90: 24022 Nonbonded interactions: 56656 Sorted by model distance: nonbonded pdb=" NH1 ARG A1034 " pdb=" OD1 ASP A1073 " model vdw 2.223 3.120 nonbonded pdb=" NZ LYS L 151 " pdb=" OE1 GLU L 197 " model vdw 2.240 3.120 nonbonded pdb=" O TYR L 50 " pdb=" OH TYR L 92 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN H 185 " pdb=" OG SER H 191 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP K 73 " pdb=" OG1 THR K 78 " model vdw 2.264 3.040 ... (remaining 56651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.007 0.100 7690 Z= 0.302 Angle : 0.892 11.782 10442 Z= 0.464 Chirality : 0.053 0.201 1177 Planarity : 0.007 0.153 1324 Dihedral : 14.411 89.455 2745 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 966 helix: 2.05 (0.28), residues: 330 sheet: -0.09 (0.31), residues: 262 loop : -1.45 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 101 TYR 0.020 0.003 TYR H 53 PHE 0.023 0.003 PHE K 68 TRP 0.016 0.003 TRP H 117 HIS 0.008 0.002 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 7683) covalent geometry : angle 0.89170 (10428) SS BOND : bond 0.01131 ( 7) SS BOND : angle 1.25504 ( 14) hydrogen bonds : bond 0.13857 ( 421) hydrogen bonds : angle 5.86051 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 28 SER cc_start: 0.7487 (p) cc_final: 0.7261 (p) REVERT: A 63 MET cc_start: 0.6307 (ppp) cc_final: 0.6016 (ppp) REVERT: A 72 ASP cc_start: 0.7305 (t70) cc_final: 0.7037 (t0) REVERT: A 169 MET cc_start: 0.7629 (tpp) cc_final: 0.7296 (ttp) REVERT: A 194 LEU cc_start: 0.7979 (mp) cc_final: 0.7514 (tt) REVERT: A 207 MET cc_start: 0.6677 (mmm) cc_final: 0.6227 (mmm) REVERT: K 102 THR cc_start: 0.6366 (t) cc_final: 0.6061 (m) outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.4495 time to fit residues: 50.1418 Evaluate side-chains 74 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 GLN L 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.209144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159812 restraints weight = 9199.726| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.04 r_work: 0.3692 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7690 Z= 0.135 Angle : 0.616 8.946 10442 Z= 0.318 Chirality : 0.042 0.170 1177 Planarity : 0.005 0.054 1324 Dihedral : 4.948 50.057 1062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.59 % Allowed : 14.67 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 966 helix: 2.72 (0.29), residues: 333 sheet: 0.12 (0.31), residues: 284 loop : -1.27 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 19 TYR 0.017 0.001 TYR A 283 PHE 0.018 0.002 PHE A 334 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7683) covalent geometry : angle 0.61555 (10428) SS BOND : bond 0.00663 ( 7) SS BOND : angle 0.72988 ( 14) hydrogen bonds : bond 0.05367 ( 421) hydrogen bonds : angle 4.36260 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 28 SER cc_start: 0.7507 (p) cc_final: 0.7302 (p) REVERT: A 63 MET cc_start: 0.6143 (ppp) cc_final: 0.5910 (ppp) REVERT: A 72 ASP cc_start: 0.7165 (t70) cc_final: 0.6893 (t0) REVERT: A 169 MET cc_start: 0.7681 (tpp) cc_final: 0.7304 (tmm) REVERT: A 194 LEU cc_start: 0.7755 (mp) cc_final: 0.7409 (tt) REVERT: A 1034 ARG cc_start: 0.8188 (ttt90) cc_final: 0.5681 (tpt170) REVERT: K 102 THR cc_start: 0.6347 (t) cc_final: 0.6032 (m) REVERT: L 82 GLU cc_start: 0.8261 (pp20) cc_final: 0.8036 (pp20) outliers start: 13 outliers final: 6 residues processed: 103 average time/residue: 0.3896 time to fit residues: 42.7119 Evaluate side-chains 80 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN H 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.205322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156825 restraints weight = 9130.849| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.35 r_work: 0.3596 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7690 Z= 0.194 Angle : 0.694 8.938 10442 Z= 0.358 Chirality : 0.045 0.186 1177 Planarity : 0.005 0.080 1324 Dihedral : 4.930 48.034 1060 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.40 % Allowed : 16.99 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 966 helix: 2.61 (0.29), residues: 333 sheet: -0.02 (0.31), residues: 279 loop : -1.38 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 19 TYR 0.022 0.002 TYR L 50 PHE 0.013 0.002 PHE A 184 TRP 0.014 0.002 TRP H 117 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7683) covalent geometry : angle 0.69408 (10428) SS BOND : bond 0.00867 ( 7) SS BOND : angle 0.81304 ( 14) hydrogen bonds : bond 0.06368 ( 421) hydrogen bonds : angle 4.51074 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6276 (ppp) cc_final: 0.5969 (ppp) REVERT: A 72 ASP cc_start: 0.7226 (t70) cc_final: 0.6965 (t0) REVERT: A 169 MET cc_start: 0.7742 (tpp) cc_final: 0.7357 (ttp) REVERT: A 194 LEU cc_start: 0.7832 (mp) cc_final: 0.7605 (tt) REVERT: A 1034 ARG cc_start: 0.8279 (ttt90) cc_final: 0.5876 (tpt170) REVERT: A 276 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7201 (tpp) REVERT: H 90 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6050 (ttm170) REVERT: K 102 THR cc_start: 0.6256 (t) cc_final: 0.5947 (m) REVERT: L 5 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7986 (mmm) REVERT: L 82 GLU cc_start: 0.8346 (pp20) cc_final: 0.8111 (pp20) REVERT: L 162 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (mt0) outliers start: 36 outliers final: 19 residues processed: 102 average time/residue: 0.4134 time to fit residues: 44.9487 Evaluate side-chains 93 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 162 GLN Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.206610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157985 restraints weight = 9249.187| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.12 r_work: 0.3635 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7690 Z= 0.158 Angle : 0.673 15.319 10442 Z= 0.344 Chirality : 0.043 0.168 1177 Planarity : 0.005 0.063 1324 Dihedral : 4.862 49.199 1060 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.28 % Allowed : 17.97 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.28), residues: 966 helix: 2.75 (0.29), residues: 327 sheet: 0.06 (0.31), residues: 288 loop : -1.37 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 19 TYR 0.018 0.002 TYR H 190 PHE 0.025 0.002 PHE A 334 TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7683) covalent geometry : angle 0.67239 (10428) SS BOND : bond 0.00807 ( 7) SS BOND : angle 1.07377 ( 14) hydrogen bonds : bond 0.05737 ( 421) hydrogen bonds : angle 4.34845 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6205 (ppp) cc_final: 0.5855 (ppp) REVERT: A 72 ASP cc_start: 0.7220 (t70) cc_final: 0.6946 (t0) REVERT: A 144 ILE cc_start: 0.6816 (pp) cc_final: 0.6378 (pt) REVERT: A 169 MET cc_start: 0.7709 (tpp) cc_final: 0.7288 (tmm) REVERT: A 1034 ARG cc_start: 0.8257 (ttt90) cc_final: 0.6277 (mtp-110) REVERT: A 276 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7168 (tpp) REVERT: H 90 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.5877 (ttm170) REVERT: H 92 GLU cc_start: 0.7287 (mp0) cc_final: 0.6724 (tm-30) REVERT: K 83 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6379 (mpt) REVERT: L 82 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: L 149 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7626 (mt0) outliers start: 35 outliers final: 13 residues processed: 97 average time/residue: 0.4827 time to fit residues: 49.6866 Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.205701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156804 restraints weight = 9184.597| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.15 r_work: 0.3613 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7690 Z= 0.174 Angle : 0.700 12.607 10442 Z= 0.355 Chirality : 0.044 0.173 1177 Planarity : 0.005 0.071 1324 Dihedral : 4.926 49.402 1060 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.52 % Allowed : 19.19 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 966 helix: 2.61 (0.29), residues: 327 sheet: 0.02 (0.30), residues: 294 loop : -1.39 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 19 TYR 0.019 0.002 TYR L 50 PHE 0.014 0.002 PHE L 211 TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7683) covalent geometry : angle 0.69896 (10428) SS BOND : bond 0.00801 ( 7) SS BOND : angle 1.30717 ( 14) hydrogen bonds : bond 0.05970 ( 421) hydrogen bonds : angle 4.37769 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6284 (ppp) cc_final: 0.5925 (ppp) REVERT: A 72 ASP cc_start: 0.7183 (t70) cc_final: 0.6911 (t0) REVERT: A 73 LEU cc_start: 0.6739 (tt) cc_final: 0.6488 (mt) REVERT: A 159 PHE cc_start: 0.7273 (t80) cc_final: 0.6925 (t80) REVERT: A 169 MET cc_start: 0.7746 (tpp) cc_final: 0.7338 (ttp) REVERT: A 1034 ARG cc_start: 0.8273 (ttt90) cc_final: 0.5961 (tpt170) REVERT: H 90 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.5797 (ttm170) REVERT: H 92 GLU cc_start: 0.7312 (mp0) cc_final: 0.6723 (tm-30) REVERT: K 27 ARG cc_start: 0.5962 (ptt180) cc_final: 0.5749 (ptt180) REVERT: K 83 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6447 (mpt) REVERT: L 18 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: L 82 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: L 149 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7656 (mt0) outliers start: 37 outliers final: 23 residues processed: 99 average time/residue: 0.4407 time to fit residues: 46.4540 Evaluate side-chains 97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 210 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.210835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161399 restraints weight = 9347.631| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.11 r_work: 0.3674 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7690 Z= 0.132 Angle : 0.634 10.653 10442 Z= 0.323 Chirality : 0.042 0.168 1177 Planarity : 0.004 0.038 1324 Dihedral : 4.672 50.607 1060 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.79 % Allowed : 20.78 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 966 helix: 2.88 (0.29), residues: 327 sheet: 0.16 (0.31), residues: 288 loop : -1.33 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 19 TYR 0.016 0.001 TYR A 283 PHE 0.030 0.002 PHE A 334 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7683) covalent geometry : angle 0.63369 (10428) SS BOND : bond 0.00658 ( 7) SS BOND : angle 0.93042 ( 14) hydrogen bonds : bond 0.05021 ( 421) hydrogen bonds : angle 4.13356 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6143 (ppp) cc_final: 0.5820 (ppp) REVERT: A 72 ASP cc_start: 0.7135 (t70) cc_final: 0.6810 (t0) REVERT: A 73 LEU cc_start: 0.6663 (tt) cc_final: 0.6404 (mt) REVERT: A 159 PHE cc_start: 0.7203 (t80) cc_final: 0.6866 (t80) REVERT: A 169 MET cc_start: 0.7775 (tpp) cc_final: 0.7300 (tmm) REVERT: A 1034 ARG cc_start: 0.8189 (ttt90) cc_final: 0.6229 (mtp-110) REVERT: A 309 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4634 (pp) REVERT: H 92 GLU cc_start: 0.7301 (mp0) cc_final: 0.6737 (tm-30) REVERT: K 83 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6308 (mpt) REVERT: L 82 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: L 149 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7669 (mt0) outliers start: 31 outliers final: 19 residues processed: 93 average time/residue: 0.5066 time to fit residues: 50.1233 Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.206484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157436 restraints weight = 9234.315| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.03 r_work: 0.3637 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7690 Z= 0.162 Angle : 0.672 9.085 10442 Z= 0.344 Chirality : 0.043 0.175 1177 Planarity : 0.004 0.040 1324 Dihedral : 4.770 49.589 1060 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.28 % Allowed : 21.39 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.28), residues: 966 helix: 2.80 (0.29), residues: 327 sheet: 0.11 (0.31), residues: 288 loop : -1.36 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 19 TYR 0.018 0.002 TYR L 50 PHE 0.015 0.002 PHE L 211 TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7683) covalent geometry : angle 0.67180 (10428) SS BOND : bond 0.00827 ( 7) SS BOND : angle 0.93652 ( 14) hydrogen bonds : bond 0.05599 ( 421) hydrogen bonds : angle 4.24370 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6255 (ppp) cc_final: 0.5881 (ppp) REVERT: A 72 ASP cc_start: 0.7189 (t70) cc_final: 0.6914 (t0) REVERT: A 159 PHE cc_start: 0.7240 (t80) cc_final: 0.6937 (t80) REVERT: A 169 MET cc_start: 0.7738 (tpp) cc_final: 0.7302 (tmm) REVERT: A 1034 ARG cc_start: 0.8278 (ttt90) cc_final: 0.6049 (tpt170) REVERT: A 309 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.4792 (pp) REVERT: H 92 GLU cc_start: 0.7288 (mp0) cc_final: 0.6729 (tm-30) REVERT: K 83 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6367 (mpt) REVERT: L 82 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (pp20) REVERT: L 149 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7646 (mt0) outliers start: 35 outliers final: 23 residues processed: 98 average time/residue: 0.4684 time to fit residues: 48.7909 Evaluate side-chains 100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.211331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163624 restraints weight = 9374.693| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.35 r_work: 0.3616 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7690 Z= 0.140 Angle : 0.648 10.933 10442 Z= 0.330 Chirality : 0.042 0.168 1177 Planarity : 0.004 0.046 1324 Dihedral : 4.676 50.249 1060 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.42 % Allowed : 22.98 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 966 helix: 2.85 (0.29), residues: 327 sheet: 0.12 (0.30), residues: 294 loop : -1.34 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 19 TYR 0.015 0.001 TYR A 283 PHE 0.034 0.002 PHE A 334 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7683) covalent geometry : angle 0.64797 (10428) SS BOND : bond 0.00630 ( 7) SS BOND : angle 0.90814 ( 14) hydrogen bonds : bond 0.05186 ( 421) hydrogen bonds : angle 4.13979 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6157 (ppp) cc_final: 0.5828 (ppp) REVERT: A 72 ASP cc_start: 0.7128 (t70) cc_final: 0.6847 (t0) REVERT: A 159 PHE cc_start: 0.7182 (t80) cc_final: 0.6885 (t80) REVERT: A 169 MET cc_start: 0.7704 (tpp) cc_final: 0.7288 (tmm) REVERT: A 1019 LYS cc_start: 0.7420 (tptp) cc_final: 0.7170 (tptp) REVERT: A 1034 ARG cc_start: 0.8152 (ttt90) cc_final: 0.5796 (tpt170) REVERT: A 309 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.4792 (pp) REVERT: H 92 GLU cc_start: 0.7242 (mp0) cc_final: 0.6786 (tm-30) REVERT: K 83 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6290 (mpt) REVERT: L 82 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7962 (pp20) REVERT: L 149 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7625 (mt0) outliers start: 28 outliers final: 20 residues processed: 90 average time/residue: 0.4924 time to fit residues: 47.0356 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.211878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.166285 restraints weight = 9285.877| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.32 r_work: 0.3653 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7690 Z= 0.136 Angle : 0.653 10.583 10442 Z= 0.330 Chirality : 0.043 0.364 1177 Planarity : 0.004 0.050 1324 Dihedral : 4.617 50.268 1060 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.79 % Allowed : 22.74 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 966 helix: 2.86 (0.29), residues: 327 sheet: 0.14 (0.30), residues: 294 loop : -1.32 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 19 TYR 0.013 0.001 TYR L 50 PHE 0.015 0.001 PHE L 211 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7683) covalent geometry : angle 0.65277 (10428) SS BOND : bond 0.00662 ( 7) SS BOND : angle 0.85505 ( 14) hydrogen bonds : bond 0.05015 ( 421) hydrogen bonds : angle 4.10708 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6113 (ppp) cc_final: 0.5760 (ppp) REVERT: A 72 ASP cc_start: 0.7091 (t70) cc_final: 0.6804 (t0) REVERT: A 159 PHE cc_start: 0.7221 (t80) cc_final: 0.6925 (t80) REVERT: A 169 MET cc_start: 0.7655 (tpp) cc_final: 0.7245 (tmm) REVERT: A 1034 ARG cc_start: 0.8200 (ttt90) cc_final: 0.5941 (tpt170) REVERT: A 309 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.4797 (pp) REVERT: H 92 GLU cc_start: 0.7184 (mp0) cc_final: 0.6748 (tm-30) REVERT: K 83 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6227 (mpt) REVERT: L 82 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: L 149 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7581 (mt0) outliers start: 31 outliers final: 21 residues processed: 94 average time/residue: 0.4485 time to fit residues: 44.8675 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 2 optimal weight: 6.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.213963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168142 restraints weight = 9345.432| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.22 r_work: 0.3688 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7690 Z= 0.124 Angle : 0.641 11.814 10442 Z= 0.322 Chirality : 0.043 0.411 1177 Planarity : 0.004 0.036 1324 Dihedral : 4.480 50.742 1060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.44 % Allowed : 24.21 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.28), residues: 966 helix: 2.92 (0.29), residues: 327 sheet: 0.19 (0.31), residues: 286 loop : -1.30 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 19 TYR 0.015 0.001 TYR A 283 PHE 0.015 0.001 PHE L 211 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7683) covalent geometry : angle 0.63789 (10428) SS BOND : bond 0.00569 ( 7) SS BOND : angle 1.71208 ( 14) hydrogen bonds : bond 0.04524 ( 421) hydrogen bonds : angle 4.01775 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.6169 (ppp) cc_final: 0.5865 (ppp) REVERT: A 72 ASP cc_start: 0.7152 (t70) cc_final: 0.6840 (t0) REVERT: A 159 PHE cc_start: 0.7232 (t80) cc_final: 0.6937 (t80) REVERT: A 169 MET cc_start: 0.7749 (tpp) cc_final: 0.7283 (tmm) REVERT: A 1034 ARG cc_start: 0.8262 (ttt90) cc_final: 0.5873 (tpt170) REVERT: A 309 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.4808 (pp) REVERT: H 92 GLU cc_start: 0.7314 (mp0) cc_final: 0.6670 (tm-30) REVERT: K 83 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6276 (mpt) REVERT: L 82 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: L 149 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7640 (mt0) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 0.4276 time to fit residues: 40.2767 Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.209931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160727 restraints weight = 9136.565| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.05 r_work: 0.3692 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7690 Z= 0.130 Angle : 0.657 11.622 10442 Z= 0.330 Chirality : 0.044 0.398 1177 Planarity : 0.004 0.034 1324 Dihedral : 4.500 50.200 1060 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 2.93 % Allowed : 24.45 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 966 helix: 2.83 (0.29), residues: 331 sheet: 0.21 (0.30), residues: 287 loop : -1.29 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 19 TYR 0.015 0.001 TYR A 283 PHE 0.015 0.001 PHE L 211 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7683) covalent geometry : angle 0.65516 (10428) SS BOND : bond 0.00608 ( 7) SS BOND : angle 1.53367 ( 14) hydrogen bonds : bond 0.04670 ( 421) hydrogen bonds : angle 4.03355 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.88 seconds wall clock time: 51 minutes 5.53 seconds (3065.53 seconds total)