Starting phenix.real_space_refine on Tue Feb 3 22:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.map" model { file = "/net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9my8_48730/02_2026/9my8_48730.cif" } resolution = 2.3 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= 0.015 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 3746 2.51 5 N 998 2.21 5 O 2635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7403 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1716 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1582 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain: "A" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 896 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1720 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 19, 'TRANS': 197} Chain: "H" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 385 Classifications: {'water': 385} Link IDs: {None: 384} Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 400 Classifications: {'water': 400} Link IDs: {None: 399} Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 520 Classifications: {'water': 520} Link IDs: {None: 519} Time building chain proxies: 1.83, per 1000 atoms: 0.25 Number of scatterers: 7403 At special positions: 0 Unit cell: (75.816, 77.274, 129.762, 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 2635 8.00 N 998 7.00 C 3746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 127 " 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: 0.51 Conformation dependent library (CDL) restraints added in 309.6 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 10.8% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 207 removed outlier: 4.339A pdb=" N GLY H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR H 206 " --> pdb=" O SER H 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.613A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.560A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.795A pdb=" N THR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.698A pdb=" N LYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 224 through 240 removed outlier: 3.961A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 8.193A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.526A pdb=" N TYR H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 137 removed outlier: 3.875A pdb=" N LEU H 156 " --> pdb=" O PHE H 137 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'L' and resid 115 through 118 removed outlier: 3.662A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.762A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.944A pdb=" N MET A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLN A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 37 removed outlier: 5.881A pdb=" N LYS B 35 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 129 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU B 114 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP B 99 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 112 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 97 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 95 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR B 116 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR B 93 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 163 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR B 56 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE B 180 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 58 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 37 removed outlier: 5.881A pdb=" N LYS B 35 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 129 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU B 114 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 71 175 hydrogen bonds defined for protein. 411 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: 1.02 Time building geometry restraints manager: 0.68 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: 1881 1.35 - 1.47: 1554 1.47 - 1.58: 2596 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6063 Sorted by residual: bond pdb=" C LYS H 216 " pdb=" N PRO H 217 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" CA VAL H 226 " pdb=" CB VAL H 226 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.31e-02 5.83e+03 2.79e+00 bond pdb=" N ASN B 105 " pdb=" CA ASN B 105 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.35e-02 5.49e+03 1.28e+00 bond pdb=" C LEU H 115 " pdb=" N ASP H 116 " ideal model delta sigma weight residual 1.324 1.352 -0.028 2.56e-02 1.53e+03 1.20e+00 bond pdb=" CB ASN B 105 " pdb=" CG ASN B 105 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 ... (remaining 6058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8059 2.09 - 4.18: 166 4.18 - 6.27: 34 6.27 - 8.36: 3 8.36 - 10.45: 1 Bond angle restraints: 8263 Sorted by residual: angle pdb=" C ALA L 84 " pdb=" CA ALA L 84 " pdb=" CB ALA L 84 " ideal model delta sigma weight residual 115.79 110.02 5.77 1.19e+00 7.06e-01 2.35e+01 angle pdb=" C ASP B 104 " pdb=" N ASN B 105 " pdb=" CA ASN B 105 " ideal model delta sigma weight residual 123.47 129.60 -6.13 1.53e+00 4.27e-01 1.61e+01 angle pdb=" C GLY B 33 " pdb=" N VAL B 34 " pdb=" CA VAL B 34 " ideal model delta sigma weight residual 120.49 125.22 -4.73 1.38e+00 5.25e-01 1.18e+01 angle pdb=" C TRP A 32 " pdb=" N ILE A 33 " pdb=" CA ILE A 33 " ideal model delta sigma weight residual 122.98 118.48 4.50 1.42e+00 4.96e-01 1.00e+01 angle pdb=" CA LEU B 195 " pdb=" CB LEU B 195 " pdb=" CG LEU B 195 " ideal model delta sigma weight residual 116.30 126.75 -10.45 3.50e+00 8.16e-02 8.91e+00 ... (remaining 8258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 3257 15.12 - 30.24: 283 30.24 - 45.36: 50 45.36 - 60.48: 15 60.48 - 75.60: 7 Dihedral angle restraints: 3612 sinusoidal: 1368 harmonic: 2244 Sorted by residual: dihedral pdb=" CA PHE H 181 " pdb=" C PHE H 181 " pdb=" N PRO H 182 " pdb=" CA PRO H 182 " ideal model delta harmonic sigma weight residual 180.00 146.84 33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 95 " pdb=" CB CYS A 95 " ideal model delta sinusoidal sigma weight residual 93.00 141.01 -48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA PHE B 141 " pdb=" C PHE B 141 " pdb=" N SER B 142 " pdb=" CA SER B 142 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 3609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 555 0.033 - 0.066: 234 0.066 - 0.100: 79 0.100 - 0.133: 46 0.133 - 0.166: 11 Chirality restraints: 925 Sorted by residual: chirality pdb=" CA ASN B 105 " pdb=" N ASN B 105 " pdb=" C ASN B 105 " pdb=" CB ASN B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE B 170 " pdb=" N ILE B 170 " pdb=" C ILE B 170 " pdb=" CB ILE B 170 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE B 224 " pdb=" N ILE B 224 " pdb=" C ILE B 224 " pdb=" CB ILE B 224 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 922 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 181 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO H 182 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 182 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO H 182 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR L 140 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO L 141 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO L 141 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 141 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 68 " -0.007 2.00e-02 2.50e+03 1.02e-02 1.83e+00 pdb=" CG PHE H 68 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE H 68 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE H 68 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE H 68 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 68 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 68 " 0.001 2.00e-02 2.50e+03 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 868 2.72 - 3.26: 7699 3.26 - 3.81: 13355 3.81 - 4.35: 16711 4.35 - 4.90: 25455 Nonbonded interactions: 64088 Sorted by model distance: nonbonded pdb=" O LEU H 81 " pdb=" O HOH H 301 " model vdw 2.172 3.040 nonbonded pdb=" O ALA B 200 " pdb=" O HOH B 401 " model vdw 2.173 3.040 nonbonded pdb=" NZ LYS L 45 " pdb=" O HOH L 301 " model vdw 2.178 3.120 nonbonded pdb=" O LEU H 115 " pdb=" O HOH H 302 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR H 105 " pdb=" O LYS A 111 " model vdw 2.207 3.040 ... (remaining 64083 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: 2.990 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.060 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6068 Z= 0.148 Angle : 0.767 10.447 8273 Z= 0.402 Chirality : 0.047 0.166 925 Planarity : 0.005 0.100 1051 Dihedral : 12.493 75.601 2165 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.08 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.72 (0.31), residues: 763 helix: -0.79 (0.85), residues: 41 sheet: -0.28 (0.34), residues: 245 loop : -0.50 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 61 TYR 0.020 0.002 TYR L 140 PHE 0.023 0.002 PHE H 68 TRP 0.020 0.002 TRP L 35 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6063) covalent geometry : angle 0.76517 ( 8263) SS BOND : bond 0.00594 ( 5) SS BOND : angle 1.57070 ( 10) hydrogen bonds : bond 0.17105 ( 168) hydrogen bonds : angle 8.31123 ( 411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4059 time to fit residues: 26.9769 Evaluate side-chains 47 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.282218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.227627 restraints weight = 6704.264| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 1.95 r_work: 0.4369 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6068 Z= 0.142 Angle : 0.720 8.223 8273 Z= 0.369 Chirality : 0.047 0.176 925 Planarity : 0.005 0.081 1051 Dihedral : 5.977 30.732 844 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.42 % Favored : 93.18 % Rotamer: Outliers : 1.37 % Allowed : 6.10 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.70 (0.30), residues: 763 helix: -0.20 (0.81), residues: 44 sheet: -0.37 (0.33), residues: 244 loop : -0.48 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 82 TYR 0.022 0.002 TYR L 140 PHE 0.015 0.002 PHE H 68 TRP 0.015 0.002 TRP A 32 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6063) covalent geometry : angle 0.71889 ( 8263) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.40766 ( 10) hydrogen bonds : bond 0.04023 ( 168) hydrogen bonds : angle 6.96976 ( 411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.278 Fit side-chains REVERT: H 132 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5671 (tttt) REVERT: L 42 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6642 (ttpt) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.3908 time to fit residues: 23.1180 Evaluate side-chains 53 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.278204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220819 restraints weight = 6600.546| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.98 r_work: 0.4312 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6068 Z= 0.176 Angle : 0.739 9.562 8273 Z= 0.383 Chirality : 0.048 0.178 925 Planarity : 0.005 0.089 1051 Dihedral : 6.166 29.829 844 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 2.29 % Allowed : 8.54 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.30), residues: 763 helix: -0.04 (0.87), residues: 40 sheet: -0.49 (0.33), residues: 243 loop : -0.40 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.026 0.002 TYR L 140 PHE 0.010 0.002 PHE B 151 TRP 0.021 0.002 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6063) covalent geometry : angle 0.73783 ( 8263) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.58127 ( 10) hydrogen bonds : bond 0.03864 ( 168) hydrogen bonds : angle 6.83316 ( 411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.271 Fit side-chains REVERT: L 42 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6448 (ttpt) REVERT: L 180 THR cc_start: 0.3506 (OUTLIER) cc_final: 0.3277 (m) REVERT: A 3 GLN cc_start: 0.6134 (pm20) cc_final: 0.4849 (tp40) REVERT: B 35 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6279 (ptpp) outliers start: 15 outliers final: 7 residues processed: 61 average time/residue: 0.3956 time to fit residues: 26.2054 Evaluate side-chains 60 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.279268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.222434 restraints weight = 6762.735| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.01 r_work: 0.4327 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6068 Z= 0.145 Angle : 0.685 9.529 8273 Z= 0.355 Chirality : 0.047 0.178 925 Planarity : 0.005 0.086 1051 Dihedral : 5.946 29.359 844 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.92 % Rotamer: Outliers : 2.29 % Allowed : 9.76 % Favored : 87.96 % 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: -0.66 (0.30), residues: 763 helix: 0.07 (0.83), residues: 44 sheet: -0.51 (0.33), residues: 245 loop : -0.37 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.023 0.002 TYR L 140 PHE 0.009 0.002 PHE B 141 TRP 0.020 0.002 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6063) covalent geometry : angle 0.68367 ( 8263) SS BOND : bond 0.00281 ( 5) SS BOND : angle 1.24149 ( 10) hydrogen bonds : bond 0.03508 ( 168) hydrogen bonds : angle 6.68406 ( 411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.273 Fit side-chains REVERT: L 42 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6399 (ttpt) REVERT: L 180 THR cc_start: 0.3439 (OUTLIER) cc_final: 0.3213 (m) REVERT: A 3 GLN cc_start: 0.6086 (pm20) cc_final: 0.4813 (tp40) REVERT: B 35 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6341 (ptpp) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.3444 time to fit residues: 22.8144 Evaluate side-chains 59 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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 = 0.4874 r_free = 0.4874 target = 0.278443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.224035 restraints weight = 6668.906| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.18 r_work: 0.4295 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6068 Z= 0.152 Angle : 0.698 8.772 8273 Z= 0.361 Chirality : 0.047 0.176 925 Planarity : 0.005 0.089 1051 Dihedral : 5.957 28.962 844 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 2.13 % Allowed : 10.37 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.30), residues: 763 helix: 0.02 (0.83), residues: 44 sheet: -0.33 (0.32), residues: 252 loop : -0.40 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.023 0.002 TYR L 140 PHE 0.021 0.002 PHE B 141 TRP 0.021 0.002 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6063) covalent geometry : angle 0.69740 ( 8263) SS BOND : bond 0.00217 ( 5) SS BOND : angle 1.27956 ( 10) hydrogen bonds : bond 0.03503 ( 168) hydrogen bonds : angle 6.63249 ( 411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.175 Fit side-chains REVERT: L 42 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6440 (ttpt) REVERT: L 180 THR cc_start: 0.3368 (OUTLIER) cc_final: 0.3157 (m) REVERT: B 35 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6339 (ptpp) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.3036 time to fit residues: 19.0521 Evaluate side-chains 58 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN B 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.275956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.218423 restraints weight = 6743.171| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.98 r_work: 0.4291 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6068 Z= 0.191 Angle : 0.756 10.602 8273 Z= 0.390 Chirality : 0.048 0.180 925 Planarity : 0.006 0.095 1051 Dihedral : 6.224 29.269 844 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.95 % Favored : 92.79 % Rotamer: Outliers : 2.90 % Allowed : 11.28 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.30), residues: 763 helix: -0.11 (0.82), residues: 44 sheet: -0.37 (0.34), residues: 239 loop : -0.34 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 196 TYR 0.026 0.002 TYR L 140 PHE 0.010 0.002 PHE L 98 TRP 0.027 0.003 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6063) covalent geometry : angle 0.75464 ( 8263) SS BOND : bond 0.00229 ( 5) SS BOND : angle 1.60197 ( 10) hydrogen bonds : bond 0.03713 ( 168) hydrogen bonds : angle 6.79644 ( 411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.278 Fit side-chains REVERT: H 115 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2959 (pp) REVERT: L 42 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6427 (ttpt) REVERT: A 3 GLN cc_start: 0.6297 (pm20) cc_final: 0.4953 (tp40) REVERT: B 35 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6314 (ptpp) outliers start: 19 outliers final: 12 residues processed: 61 average time/residue: 0.3447 time to fit residues: 23.0508 Evaluate side-chains 62 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4863 r_free = 0.4863 target = 0.276570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220093 restraints weight = 6740.770| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 1.96 r_work: 0.4303 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6068 Z= 0.167 Angle : 0.723 9.634 8273 Z= 0.375 Chirality : 0.047 0.171 925 Planarity : 0.005 0.087 1051 Dihedral : 6.085 28.651 844 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.92 % Rotamer: Outliers : 3.35 % Allowed : 10.82 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.30), residues: 763 helix: -0.14 (0.82), residues: 44 sheet: -0.36 (0.34), residues: 241 loop : -0.34 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.025 0.002 TYR L 140 PHE 0.009 0.001 PHE L 209 TRP 0.025 0.002 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6063) covalent geometry : angle 0.72230 ( 8263) SS BOND : bond 0.00237 ( 5) SS BOND : angle 1.34489 ( 10) hydrogen bonds : bond 0.03653 ( 168) hydrogen bonds : angle 6.71104 ( 411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.255 Fit side-chains REVERT: H 115 LEU cc_start: 0.3195 (OUTLIER) cc_final: 0.2953 (pp) REVERT: L 42 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6471 (ttpt) REVERT: A 3 GLN cc_start: 0.6210 (pm20) cc_final: 0.4872 (tp40) REVERT: B 35 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6292 (ptpp) outliers start: 22 outliers final: 15 residues processed: 62 average time/residue: 0.3638 time to fit residues: 24.5120 Evaluate side-chains 67 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.279326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.243247 restraints weight = 6782.482| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 1.94 r_work: 0.4317 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6068 Z= 0.135 Angle : 0.678 9.122 8273 Z= 0.351 Chirality : 0.046 0.178 925 Planarity : 0.005 0.078 1051 Dihedral : 5.828 27.435 844 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.08 % Favored : 92.66 % Rotamer: Outliers : 2.44 % Allowed : 11.89 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.31), residues: 763 helix: -0.00 (0.84), residues: 44 sheet: -0.13 (0.33), residues: 247 loop : -0.39 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 166 TYR 0.021 0.002 TYR L 140 PHE 0.009 0.001 PHE L 209 TRP 0.024 0.002 TRP A 32 HIS 0.002 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6063) covalent geometry : angle 0.67686 ( 8263) SS BOND : bond 0.00224 ( 5) SS BOND : angle 1.09104 ( 10) hydrogen bonds : bond 0.03353 ( 168) hydrogen bonds : angle 6.48548 ( 411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.178 Fit side-chains REVERT: H 19 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6497 (ttp-110) REVERT: L 42 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6423 (ttpt) REVERT: A 3 GLN cc_start: 0.6225 (pm20) cc_final: 0.4960 (tp40) REVERT: B 35 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6326 (ptpp) outliers start: 16 outliers final: 13 residues processed: 59 average time/residue: 0.3411 time to fit residues: 21.8058 Evaluate side-chains 63 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4881 r_free = 0.4881 target = 0.278930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.228111 restraints weight = 6699.346| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 2.00 r_work: 0.4298 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6068 Z= 0.143 Angle : 0.694 8.973 8273 Z= 0.358 Chirality : 0.047 0.165 925 Planarity : 0.005 0.079 1051 Dihedral : 5.793 26.713 844 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 2.59 % Allowed : 12.35 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.31), residues: 763 helix: -0.12 (0.88), residues: 40 sheet: -0.27 (0.34), residues: 240 loop : -0.28 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.022 0.002 TYR L 140 PHE 0.009 0.001 PHE L 209 TRP 0.021 0.002 TRP A 32 HIS 0.002 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6063) covalent geometry : angle 0.69351 ( 8263) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.19114 ( 10) hydrogen bonds : bond 0.03365 ( 168) hydrogen bonds : angle 6.45084 ( 411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.300 Fit side-chains REVERT: H 19 ARG cc_start: 0.7168 (ttt90) cc_final: 0.6485 (ttp-110) REVERT: L 42 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6449 (ttpt) REVERT: L 164 THR cc_start: 0.3106 (p) cc_final: 0.2783 (p) REVERT: A 3 GLN cc_start: 0.6188 (pm20) cc_final: 0.4905 (tp40) REVERT: B 153 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6367 (mtm) outliers start: 17 outliers final: 14 residues processed: 60 average time/residue: 0.4713 time to fit residues: 30.6069 Evaluate side-chains 67 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4868 r_free = 0.4868 target = 0.277135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.223739 restraints weight = 6670.822| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.07 r_work: 0.4288 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6068 Z= 0.169 Angle : 0.735 9.578 8273 Z= 0.378 Chirality : 0.048 0.217 925 Planarity : 0.005 0.082 1051 Dihedral : 5.980 27.033 844 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.95 % Favored : 92.79 % Rotamer: Outliers : 2.59 % Allowed : 12.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.30), residues: 763 helix: -0.39 (0.84), residues: 42 sheet: -0.32 (0.34), residues: 240 loop : -0.33 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.023 0.002 TYR L 140 PHE 0.009 0.001 PHE L 209 TRP 0.026 0.002 TRP A 32 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6063) covalent geometry : angle 0.73298 ( 8263) SS BOND : bond 0.00287 ( 5) SS BOND : angle 1.54877 ( 10) hydrogen bonds : bond 0.03573 ( 168) hydrogen bonds : angle 6.60237 ( 411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.305 Fit side-chains REVERT: L 42 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6448 (ttpt) REVERT: A 3 GLN cc_start: 0.6217 (pm20) cc_final: 0.4917 (tp40) outliers start: 17 outliers final: 15 residues processed: 56 average time/residue: 0.4608 time to fit residues: 28.0232 Evaluate side-chains 62 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4895 r_free = 0.4895 target = 0.280870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.230121 restraints weight = 6730.210| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 1.99 r_work: 0.4328 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6068 Z= 0.125 Angle : 0.665 8.801 8273 Z= 0.344 Chirality : 0.046 0.192 925 Planarity : 0.005 0.072 1051 Dihedral : 5.621 25.903 844 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.95 % Favored : 92.79 % Rotamer: Outliers : 2.59 % Allowed : 12.20 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.31), residues: 763 helix: -0.27 (0.86), residues: 42 sheet: -0.29 (0.34), residues: 241 loop : -0.28 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.019 0.001 TYR L 140 PHE 0.010 0.001 PHE L 209 TRP 0.020 0.002 TRP A 32 HIS 0.002 0.000 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6063) covalent geometry : angle 0.66397 ( 8263) SS BOND : bond 0.00256 ( 5) SS BOND : angle 1.11572 ( 10) hydrogen bonds : bond 0.03198 ( 168) hydrogen bonds : angle 6.30975 ( 411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.50 seconds wall clock time: 47 minutes 52.82 seconds (2872.82 seconds total)