Starting phenix.real_space_refine on Fri Sep 11 12:59:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.cif" model { file = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tyi_20583/09_2026/6tyi_20583.cif" } resolution = 3.3 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= 0.008 sd= 0.148 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 C 5894 2.51 5 N 1567 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9184 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain: "Y" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 236 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.22 Number of scatterers: 9184 At special positions: 0 Unit cell: (84.8, 84.8, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 4 15.00 O 1683 8.00 N 1567 7.00 C 5894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 374.2 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 21 through 63 removed outlier: 4.514A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 103 through 128 Processing helix chain 'A' and resid 129 through 159 removed outlier: 3.913A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 176 through 233 Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 11 through 18 removed outlier: 3.597A pdb=" N HIS B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 63 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 82 through 98 removed outlier: 4.075A pdb=" N LEU B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 removed outlier: 3.694A pdb=" N ILE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 162 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 170 through 233 removed outlier: 3.754A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 20 through 63 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 103 through 127 Processing helix chain 'C' and resid 129 through 163 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 170 through 232 removed outlier: 3.567A pdb=" N ILE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 21 through 63 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 82 through 98 Processing helix chain 'D' and resid 103 through 128 Processing helix chain 'D' and resid 129 through 161 removed outlier: 4.063A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 170 through 233 removed outlier: 3.666A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.662A pdb=" N MET E 15 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR E 16 " --> pdb=" O TRP E 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 12 through 16' Processing helix chain 'E' and resid 23 through 63 removed outlier: 4.278A pdb=" N GLY E 29 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 82 through 98 Processing helix chain 'E' and resid 103 through 127 Processing helix chain 'E' and resid 129 through 162 Proline residue: E 141 - end of helix removed outlier: 3.813A pdb=" N ALA E 160 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR E 162 " --> pdb=" O GLY E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 233 removed outlier: 3.658A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Proline residue: E 190 - end of helix Processing helix chain 'Y' and resid 20 through 37 removed outlier: 3.962A pdb=" N VAL Y 26 " --> pdb=" O PRO Y 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET Y 27 " --> pdb=" O PHE Y 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Y 29 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE Y 34 " --> pdb=" O LEU Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 42 Processing helix chain 'Z' and resid 23 through 36 removed outlier: 3.735A pdb=" N MET Z 27 " --> pdb=" O PHE Z 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL Z 36 " --> pdb=" O ILE Z 32 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2442 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: 1.43 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1524 1.30 - 1.43: 2284 1.43 - 1.55: 5412 1.55 - 1.68: 30 1.68 - 1.80: 67 Bond restraints: 9317 Sorted by residual: bond pdb=" C11 PGT A 301 " pdb=" O3 PGT A 301 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C31 PGT A 301 " pdb=" O2 PGT A 301 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 PEV C 301 " pdb=" O2 PEV C 301 " ideal model delta sigma weight residual 1.330 1.403 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 PEV E 301 " pdb=" O2 PEV E 301 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 PEV C 301 " pdb=" O3 PEV C 301 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.83e+00 ... (remaining 9312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12415 3.73 - 7.47: 140 7.47 - 11.20: 9 11.20 - 14.93: 0 14.93 - 18.66: 6 Bond angle restraints: 12570 Sorted by residual: angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.48 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PEV C 301 " pdb=" P PEV C 301 " pdb=" O2P PEV C 301 " ideal model delta sigma weight residual 119.37 100.88 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" O3P PEV C 301 " pdb=" P PEV C 301 " pdb=" O4P PEV C 301 " ideal model delta sigma weight residual 93.57 111.90 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" O1P PGT A 301 " pdb=" P PGT A 301 " pdb=" O2P PGT A 301 " ideal model delta sigma weight residual 119.10 100.80 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" O3P PEV E 301 " pdb=" P PEV E 301 " pdb=" O4P PEV E 301 " ideal model delta sigma weight residual 93.57 111.77 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4838 16.84 - 33.67: 535 33.67 - 50.51: 143 50.51 - 67.35: 32 67.35 - 84.19: 15 Dihedral angle restraints: 5563 sinusoidal: 2191 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ALA A 19 " pdb=" C ALA A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASP Z 17 " pdb=" C ASP Z 17 " pdb=" N ILE Z 18 " pdb=" CA ILE Z 18 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA E 19 " pdb=" C ALA E 19 " pdb=" N ASP E 20 " pdb=" CA ASP E 20 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 968 0.046 - 0.092: 424 0.092 - 0.138: 60 0.138 - 0.184: 10 0.184 - 0.230: 3 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C5 PGT A 301 " pdb=" C4 PGT A 301 " pdb=" C6 PGT A 301 " pdb=" O5 PGT A 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PGT A 301 " pdb=" C1 PGT A 301 " pdb=" C3 PGT A 301 " pdb=" O2 PGT A 301 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1462 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " 0.017 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 113 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 140 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 171 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO E 172 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " -0.022 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 21 2.42 - 3.04: 6027 3.04 - 3.66: 13193 3.66 - 4.28: 19345 4.28 - 4.90: 32973 Nonbonded interactions: 71559 Sorted by model distance: nonbonded pdb=" OG SER D 98 " pdb=" NH1 ARG D 110 " model vdw 1.796 3.120 nonbonded pdb=" OG SER A 98 " pdb=" NH1 ARG A 110 " model vdw 2.179 3.120 nonbonded pdb=" OE2 GLU A 58 " pdb=" OG SER A 82 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 148 " pdb=" O ALA A 177 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU B 58 " pdb=" OG SER B 82 " model vdw 2.241 3.040 ... (remaining 71554 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 233) selection = (chain 'B' and resid 11 through 233) selection = (chain 'C' and resid 11 through 233) selection = (chain 'D' and resid 11 through 233) selection = (chain 'E' and resid 11 through 233) } ncs_group { reference = (chain 'Y' and resid 12 through 40) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.730 Find NCS groups from input model: 0.240 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.015 0.798 9319 Z= 1.083 Angle : 1.033 18.665 12570 Z= 0.504 Chirality : 0.049 0.230 1465 Planarity : 0.004 0.039 1598 Dihedral : 15.885 84.185 3385 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 0.43 % Allowed : 10.99 % Favored : 88.58 % 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: -0.84 (0.22), residues: 1172 helix: 0.18 (0.15), residues: 996 sheet: None (None), residues: 0 loop : -4.46 (0.30), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 118 TYR 0.016 0.002 TYR D 132 PHE 0.040 0.003 PHE A 113 TRP 0.012 0.002 TRP E 38 HIS 0.009 0.001 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.48 ( 9317) covalent geometry : angle 1.03303 / 0.50 (12570) hydrogen bonds : bond 0.09594 / 6.42 ( 816) hydrogen bonds : angle 4.30293 / 3.17 ( 2442) Misc. bond : bond 0.66393 / 32.58 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.347 Fit side-chains REVERT: A 94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8202 (tp30) REVERT: B 126 MET cc_start: 0.8050 (mmm) cc_final: 0.7532 (mmt) REVERT: C 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 94 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5210 (mm-30) REVERT: D 128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7521 (ttp-110) REVERT: E 226 LEU cc_start: 0.8851 (mt) cc_final: 0.8548 (mp) outliers start: 4 outliers final: 3 residues processed: 152 average time/residue: 0.1265 time to fit residues: 25.1799 Evaluate side-chains 126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN B 70 GLN B 93 ASN C 215 GLN D 93 ASN D 125 GLN D 196 ASN E 69 ASN E 93 ASN E 196 ASN Z 16 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133731 restraints weight = 10099.629| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.92 r_work: 0.3378 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9319 Z= 0.138 Angle : 0.517 6.800 12570 Z= 0.266 Chirality : 0.035 0.121 1465 Planarity : 0.003 0.029 1598 Dihedral : 9.724 58.348 1392 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 16.06 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1172 helix: 2.05 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -4.19 (0.35), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.009 0.001 TYR C 132 PHE 0.018 0.001 PHE A 113 TRP 0.012 0.001 TRP E 38 HIS 0.003 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9317) covalent geometry : angle 0.51662 / 0.27 (12570) hydrogen bonds : bond 0.05421 / 3.65 ( 816) hydrogen bonds : angle 3.45537 / 2.55 ( 2442) Misc. bond : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 94 GLU cc_start: 0.8909 (tp30) cc_final: 0.8705 (tp30) REVERT: B 96 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 126 MET cc_start: 0.7652 (mmm) cc_final: 0.7406 (mmt) REVERT: B 153 MET cc_start: 0.8560 (ttp) cc_final: 0.8232 (ttt) REVERT: C 93 ASN cc_start: 0.8401 (t0) cc_final: 0.7926 (t0) REVERT: C 118 ARG cc_start: 0.7250 (tpm170) cc_final: 0.6871 (mmm-85) REVERT: D 200 ARG cc_start: 0.8107 (mmm160) cc_final: 0.6881 (mtp180) REVERT: E 58 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7923 (mt-10) REVERT: E 226 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (mp) REVERT: Z 15 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7867 (mtt) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 0.1236 time to fit residues: 20.0852 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Z residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.170895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135484 restraints weight = 10248.507| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9319 Z= 0.133 Angle : 0.492 6.785 12570 Z= 0.249 Chirality : 0.035 0.129 1465 Planarity : 0.003 0.056 1598 Dihedral : 9.164 59.981 1391 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 17.24 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.25), residues: 1172 helix: 2.72 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -3.87 (0.37), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.008 0.001 TYR D 132 PHE 0.015 0.001 PHE A 113 TRP 0.011 0.001 TRP E 38 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9317) covalent geometry : angle 0.49191 / 0.25 (12570) hydrogen bonds : bond 0.05087 / 3.42 ( 816) hydrogen bonds : angle 3.29506 / 2.43 ( 2442) Misc. bond : bond 0.00244 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8248 (pt0) REVERT: B 94 GLU cc_start: 0.8900 (tp30) cc_final: 0.8604 (tp30) REVERT: B 96 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 126 MET cc_start: 0.7637 (mmm) cc_final: 0.7345 (mmt) REVERT: B 153 MET cc_start: 0.8584 (ttp) cc_final: 0.8213 (ttt) REVERT: C 118 ARG cc_start: 0.7392 (tpm170) cc_final: 0.6959 (mmm-85) REVERT: D 200 ARG cc_start: 0.8079 (mmm160) cc_final: 0.6911 (mtp180) REVERT: E 99 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: E 226 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8146 (mp) REVERT: Z 15 MET cc_start: 0.8169 (mtm) cc_final: 0.7862 (mtt) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.1261 time to fit residues: 19.8466 Evaluate side-chains 116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.188775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153905 restraints weight = 10069.963| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.88 r_work: 0.3653 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9319 Z= 0.124 Angle : 0.472 6.800 12570 Z= 0.239 Chirality : 0.034 0.120 1465 Planarity : 0.003 0.041 1598 Dihedral : 8.728 59.796 1391 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.69 % Allowed : 17.56 % Favored : 79.74 % 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: 3.46 (0.25), residues: 1172 helix: 3.08 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -3.65 (0.38), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.007 0.001 TYR B 132 PHE 0.013 0.001 PHE A 113 TRP 0.010 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9317) covalent geometry : angle 0.47228 / 0.24 (12570) hydrogen bonds : bond 0.04727 / 3.18 ( 816) hydrogen bonds : angle 3.17822 / 2.34 ( 2442) Misc. bond : bond 0.00292 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8113 (pt0) REVERT: A 94 GLU cc_start: 0.8607 (tp30) cc_final: 0.7909 (tp30) REVERT: A 223 ASP cc_start: 0.7844 (m-30) cc_final: 0.7517 (m-30) REVERT: B 96 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7791 (mt-10) REVERT: B 153 MET cc_start: 0.8467 (ttp) cc_final: 0.8076 (ttt) REVERT: C 114 ARG cc_start: 0.6322 (tpm170) cc_final: 0.6030 (tpm170) REVERT: C 118 ARG cc_start: 0.7194 (tpm170) cc_final: 0.6991 (mmm-85) REVERT: D 153 MET cc_start: 0.6912 (ttp) cc_final: 0.6635 (ttt) REVERT: D 200 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7011 (mtm-85) REVERT: E 215 GLN cc_start: 0.8171 (tp40) cc_final: 0.7608 (tt0) REVERT: E 226 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8206 (mp) REVERT: Z 15 MET cc_start: 0.7824 (mtm) cc_final: 0.7602 (mtt) outliers start: 25 outliers final: 14 residues processed: 129 average time/residue: 0.1141 time to fit residues: 20.0153 Evaluate side-chains 116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.188280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153188 restraints weight = 9967.026| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.87 r_work: 0.3646 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9319 Z= 0.134 Angle : 0.487 7.017 12570 Z= 0.244 Chirality : 0.035 0.163 1465 Planarity : 0.003 0.060 1598 Dihedral : 8.545 59.496 1390 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.48 % Allowed : 18.32 % Favored : 79.20 % 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: 3.64 (0.25), residues: 1172 helix: 3.18 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : -3.47 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.009 0.001 TYR B 16 PHE 0.010 0.001 PHE Z 23 TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9317) covalent geometry : angle 0.48691 / 0.24 (12570) hydrogen bonds : bond 0.04835 / 3.25 ( 816) hydrogen bonds : angle 3.17524 / 2.33 ( 2442) Misc. bond : bond 0.00229 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.347 Fit side-chains REVERT: A 64 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8061 (pt0) REVERT: A 223 ASP cc_start: 0.7826 (m-30) cc_final: 0.7414 (m-30) REVERT: B 96 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 153 MET cc_start: 0.8471 (ttp) cc_final: 0.8074 (ttt) REVERT: C 114 ARG cc_start: 0.6348 (tpm170) cc_final: 0.6044 (tpm170) REVERT: C 118 ARG cc_start: 0.7236 (tpm170) cc_final: 0.6915 (mmm-85) REVERT: D 128 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7303 (ttp-170) REVERT: D 153 MET cc_start: 0.6922 (ttp) cc_final: 0.6658 (ttt) REVERT: D 200 ARG cc_start: 0.7848 (mmm160) cc_final: 0.6928 (mtp180) REVERT: E 99 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: E 215 GLN cc_start: 0.8165 (tp40) cc_final: 0.7604 (tt0) REVERT: E 226 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8207 (mp) REVERT: Z 15 MET cc_start: 0.7870 (mtm) cc_final: 0.7630 (mtt) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.1133 time to fit residues: 19.1017 Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 166 ASN E 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153897 restraints weight = 10021.155| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.87 r_work: 0.3658 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9319 Z= 0.122 Angle : 0.467 7.389 12570 Z= 0.236 Chirality : 0.034 0.130 1465 Planarity : 0.003 0.047 1598 Dihedral : 8.252 59.684 1390 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.69 % Allowed : 18.97 % Favored : 78.34 % 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: 3.83 (0.25), residues: 1172 helix: 3.29 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.34 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.006 0.001 TYR B 132 PHE 0.010 0.001 PHE Z 23 TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS D 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9317) covalent geometry : angle 0.46697 / 0.24 (12570) hydrogen bonds : bond 0.04596 / 3.09 ( 816) hydrogen bonds : angle 3.11478 / 2.28 ( 2442) Misc. bond : bond 0.00189 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8089 (pt0) REVERT: A 223 ASP cc_start: 0.7808 (m-30) cc_final: 0.7394 (m-30) REVERT: B 153 MET cc_start: 0.8454 (ttp) cc_final: 0.8056 (ttt) REVERT: C 118 ARG cc_start: 0.7103 (tpm170) cc_final: 0.6893 (mmm-85) REVERT: D 128 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7246 (ttp-170) REVERT: D 153 MET cc_start: 0.6904 (ttp) cc_final: 0.6620 (ttt) REVERT: D 200 ARG cc_start: 0.7844 (mmm160) cc_final: 0.6938 (mtp180) REVERT: E 93 ASN cc_start: 0.8777 (t0) cc_final: 0.8561 (t0) REVERT: E 94 GLU cc_start: 0.8433 (tp30) cc_final: 0.7885 (tp30) REVERT: E 99 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: E 208 MET cc_start: 0.8146 (ttp) cc_final: 0.7942 (ttm) REVERT: E 226 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 25 outliers final: 17 residues processed: 124 average time/residue: 0.1174 time to fit residues: 19.5748 Evaluate side-chains 120 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.197381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160446 restraints weight = 10106.265| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.94 r_work: 0.3651 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9319 Z= 0.123 Angle : 0.465 8.010 12570 Z= 0.235 Chirality : 0.034 0.119 1465 Planarity : 0.003 0.063 1598 Dihedral : 7.969 57.364 1390 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.59 % Allowed : 18.53 % Favored : 78.88 % 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: 3.95 (0.25), residues: 1172 helix: 3.36 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.24 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 54 TYR 0.006 0.001 TYR C 132 PHE 0.010 0.001 PHE Z 23 TRP 0.009 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9317) covalent geometry : angle 0.46477 / 0.24 (12570) hydrogen bonds : bond 0.04557 / 3.07 ( 816) hydrogen bonds : angle 3.08212 / 2.26 ( 2442) Misc. bond : bond 0.00170 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8095 (pt0) REVERT: A 181 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7519 (m) REVERT: A 223 ASP cc_start: 0.7790 (m-30) cc_final: 0.7339 (m-30) REVERT: B 153 MET cc_start: 0.8439 (ttp) cc_final: 0.8034 (ttt) REVERT: C 64 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 128 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7145 (ttp-170) REVERT: D 153 MET cc_start: 0.6900 (ttp) cc_final: 0.6620 (ttt) REVERT: D 200 ARG cc_start: 0.7616 (mmm160) cc_final: 0.6779 (mtm110) REVERT: E 99 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: E 226 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8158 (mp) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1187 time to fit residues: 20.0544 Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.190819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156001 restraints weight = 9945.522| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.86 r_work: 0.3683 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9319 Z= 0.117 Angle : 0.467 8.135 12570 Z= 0.235 Chirality : 0.034 0.117 1465 Planarity : 0.003 0.056 1598 Dihedral : 7.542 59.321 1389 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 19.29 % Favored : 78.34 % 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: 4.07 (0.25), residues: 1172 helix: 3.44 (0.15), residues: 1018 sheet: None (None), residues: 0 loop : -3.22 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.007 0.001 TYR B 132 PHE 0.010 0.001 PHE Z 23 TRP 0.008 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9317) covalent geometry : angle 0.46718 / 0.24 (12570) hydrogen bonds : bond 0.04382 / 2.95 ( 816) hydrogen bonds : angle 3.03842 / 2.22 ( 2442) Misc. bond : bond 0.00176 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8090 (pt0) REVERT: A 181 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7602 (m) REVERT: A 223 ASP cc_start: 0.7782 (m-30) cc_final: 0.7354 (m-30) REVERT: B 153 MET cc_start: 0.8436 (ttp) cc_final: 0.8036 (ttt) REVERT: C 64 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 118 ARG cc_start: 0.7083 (tpm170) cc_final: 0.6848 (mmm-85) REVERT: D 128 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7115 (ttp-170) REVERT: D 153 MET cc_start: 0.6956 (ttp) cc_final: 0.6677 (ttt) REVERT: D 200 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6587 (mtm110) REVERT: E 99 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: Z 15 MET cc_start: 0.6878 (mmt) cc_final: 0.6301 (mmt) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.1204 time to fit residues: 19.3731 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.197841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161023 restraints weight = 10116.814| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.93 r_work: 0.3661 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9319 Z= 0.124 Angle : 0.473 8.278 12570 Z= 0.238 Chirality : 0.034 0.118 1465 Planarity : 0.003 0.071 1598 Dihedral : 7.310 51.633 1389 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 19.29 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.25), residues: 1172 helix: 3.43 (0.15), residues: 1018 sheet: None (None), residues: 0 loop : -3.17 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 54 TYR 0.006 0.001 TYR D 132 PHE 0.011 0.001 PHE Z 23 TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9317) covalent geometry : angle 0.47260 / 0.24 (12570) hydrogen bonds : bond 0.04536 / 3.05 ( 816) hydrogen bonds : angle 3.05715 / 2.24 ( 2442) Misc. bond : bond 0.00174 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8073 (pt0) REVERT: A 181 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7680 (m) REVERT: A 223 ASP cc_start: 0.7772 (m-30) cc_final: 0.7315 (m-30) REVERT: B 153 MET cc_start: 0.8437 (ttp) cc_final: 0.8030 (ttt) REVERT: C 64 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 153 MET cc_start: 0.6969 (ttp) cc_final: 0.6703 (ttt) REVERT: D 200 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6659 (mtm110) REVERT: E 99 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7457 (pt0) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.1099 time to fit residues: 18.2917 Evaluate side-chains 122 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155867 restraints weight = 9889.683| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.86 r_work: 0.3679 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9319 Z= 0.120 Angle : 0.470 8.334 12570 Z= 0.238 Chirality : 0.034 0.117 1465 Planarity : 0.003 0.066 1598 Dihedral : 7.068 51.601 1389 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.48 % Allowed : 19.83 % Favored : 77.69 % 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: 4.16 (0.25), residues: 1172 helix: 3.50 (0.15), residues: 1017 sheet: None (None), residues: 0 loop : -3.15 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.015 0.001 TYR C 16 PHE 0.010 0.001 PHE Z 23 TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9317) covalent geometry : angle 0.46967 / 0.24 (12570) hydrogen bonds : bond 0.04432 / 2.99 ( 816) hydrogen bonds : angle 3.03608 / 2.22 ( 2442) Misc. bond : bond 0.00175 / 0.09 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8068 (pt0) REVERT: A 118 ARG cc_start: 0.7242 (mtp180) cc_final: 0.7034 (ttt180) REVERT: A 181 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7678 (m) REVERT: A 223 ASP cc_start: 0.7757 (m-30) cc_final: 0.7300 (m-30) REVERT: B 153 MET cc_start: 0.8376 (ttp) cc_final: 0.7971 (ttt) REVERT: C 64 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 153 MET cc_start: 0.6959 (ttp) cc_final: 0.6681 (ttt) REVERT: D 200 ARG cc_start: 0.7268 (mmm160) cc_final: 0.6627 (mtm110) REVERT: E 99 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7556 (pt0) outliers start: 23 outliers final: 20 residues processed: 119 average time/residue: 0.1094 time to fit residues: 17.7974 Evaluate side-chains 122 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.187008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151649 restraints weight = 9973.815| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.89 r_work: 0.3634 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9319 Z= 0.147 Angle : 0.505 8.037 12570 Z= 0.254 Chirality : 0.035 0.118 1465 Planarity : 0.003 0.065 1598 Dihedral : 7.214 51.538 1389 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.59 % Allowed : 19.83 % Favored : 77.59 % 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: 3.99 (0.25), residues: 1172 helix: 3.36 (0.15), residues: 1018 sheet: None (None), residues: 0 loop : -3.10 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 54 TYR 0.014 0.001 TYR C 16 PHE 0.010 0.001 PHE Z 23 TRP 0.010 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9317) covalent geometry : angle 0.50474 / 0.25 (12570) hydrogen bonds : bond 0.04956 / 3.34 ( 816) hydrogen bonds : angle 3.13444 / 2.30 ( 2442) Misc. bond : bond 0.00186 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.54 seconds wall clock time: 32 minutes 30.40 seconds (1950.40 seconds total)