Starting phenix.real_space_refine on Thu Sep 18 21:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.275 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9j_5778/09_2025/3j9j_5778.map" } resolution = 3.275 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 ------------------------------------------------------------------------------- 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= 1.000 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 S 80 5.16 5 C 6952 2.51 5 N 1608 2.21 5 O 1804 1.98 5 H 10624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21068 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Restraints were copied for chains: B, C, D Time building chain proxies: 5.06, per 1000 atoms: 0.24 Number of scatterers: 21068 At special positions: 0 Unit cell: (117.913, 117.913, 82.6608, 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 80 16.00 O 1804 8.00 N 1608 7.00 C 6952 6.00 H 10624 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 593.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 74 Processing helix chain 'A' and resid 88 through 119 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.772A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 74 Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 130 through 152 removed outlier: 4.390A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.850A pdb=" N PHE B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 287 through 309 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 49 through 74 Processing helix chain 'C' and resid 88 through 119 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 206 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.852A pdb=" N PHE C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 268 Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 287 through 309 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 49 through 74 Processing helix chain 'D' and resid 88 through 119 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 130 through 152 removed outlier: 4.392A pdb=" N PHE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 206 " --> pdb=" O PHE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 268 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 287 through 309 760 hydrogen bonds defined for protein. 2208 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: 4.71 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10600 1.13 - 1.30: 1564 1.30 - 1.47: 4509 1.47 - 1.64: 4515 1.64 - 1.81: 136 Bond restraints: 21324 Sorted by residual: bond pdb=" CE1 HIS A 30 " pdb=" HE1 HIS A 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 HIS C 30 " pdb=" HE1 HIS C 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 TYR B 131 " pdb=" HE1 TYR B 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" CE1 TYR A 131 " pdb=" HE1 TYR A 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CZ2 TRP C 294 " pdb=" HZ2 TRP C 294 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 34267 2.66 - 5.32: 3235 5.32 - 7.98: 898 7.98 - 10.64: 8 10.64 - 13.31: 24 Bond angle restraints: 38432 Sorted by residual: angle pdb=" C ARG B 120 " pdb=" N PRO B 121 " pdb=" CA PRO B 121 " ideal model delta sigma weight residual 119.28 127.05 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" C ARG D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta sigma weight residual 119.28 127.04 -7.76 1.10e+00 8.26e-01 4.98e+01 angle pdb=" C ARG A 120 " pdb=" N PRO A 121 " pdb=" CA PRO A 121 " ideal model delta sigma weight residual 119.28 127.01 -7.73 1.10e+00 8.26e-01 4.93e+01 angle pdb=" C ARG C 120 " pdb=" N PRO C 121 " pdb=" CA PRO C 121 " ideal model delta sigma weight residual 119.28 126.97 -7.69 1.10e+00 8.26e-01 4.89e+01 angle pdb=" C LEU D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.03e+00 9.43e-01 4.50e+01 ... (remaining 38427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 9433 13.30 - 26.61: 311 26.61 - 39.91: 68 39.91 - 53.21: 98 53.21 - 66.51: 130 Dihedral angle restraints: 10040 sinusoidal: 5252 harmonic: 4788 Sorted by residual: dihedral pdb=" CB MET D 182 " pdb=" CG MET D 182 " pdb=" SD MET D 182 " pdb=" CE MET D 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.64 -39.64 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET C 182 " pdb=" CG MET C 182 " pdb=" SD MET C 182 " pdb=" CE MET C 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.63 -39.63 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET A 182 " pdb=" CG MET A 182 " pdb=" SD MET A 182 " pdb=" CE MET A 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.62 -39.62 3 1.50e+01 4.44e-03 7.03e+00 ... (remaining 10037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 566 0.047 - 0.093: 570 0.093 - 0.140: 323 0.140 - 0.186: 106 0.186 - 0.233: 59 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA PHE A 309 " pdb=" N PHE A 309 " pdb=" C PHE A 309 " pdb=" CB PHE A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE B 309 " pdb=" N PHE B 309 " pdb=" C PHE B 309 " pdb=" CB PHE B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PHE D 309 " pdb=" N PHE D 309 " pdb=" C PHE D 309 " pdb=" CB PHE D 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1621 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 30 " 0.057 2.00e-02 2.50e+03 4.44e-02 4.43e+01 pdb=" CG HIS D 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS D 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS D 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS D 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS D 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS D 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS D 30 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 30 " -0.057 2.00e-02 2.50e+03 4.43e-02 4.42e+01 pdb=" CG HIS A 30 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS A 30 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 30 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 30 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 30 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS A 30 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS A 30 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 30 " 0.057 2.00e-02 2.50e+03 4.42e-02 4.40e+01 pdb=" CG HIS B 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS B 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS B 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS B 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 30 " 0.042 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 710 2.01 - 2.66: 28402 2.66 - 3.30: 66390 3.30 - 3.95: 84546 3.95 - 4.60: 128117 Nonbonded interactions: 308165 Sorted by model distance: nonbonded pdb=" OE1 GLU D 156 " pdb=" H GLU D 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU C 156 " pdb=" H GLU C 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU A 156 " pdb=" H GLU A 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU A 11 " pdb=" H GLU A 11 " model vdw 1.522 2.450 ... (remaining 308160 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.550 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.320 Find NCS groups from input model: 0.140 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 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 0.063 10700 Z= 0.974 Angle : 1.078 9.580 14452 Z= 0.764 Chirality : 0.089 0.233 1624 Planarity : 0.010 0.126 1756 Dihedral : 9.349 66.513 3880 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 2.24 % Allowed : 3.27 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: -0.65 (0.22), residues: 1252 helix: -0.21 (0.15), residues: 964 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 314 TYR 0.044 0.005 TYR D 250 PHE 0.023 0.004 PHE A 256 TRP 0.035 0.010 TRP D 294 HIS 0.002 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.01484 (10700) covalent geometry : angle 1.07839 (14452) hydrogen bonds : bond 0.16613 ( 760) hydrogen bonds : angle 5.87144 ( 2208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 MET cc_start: 0.5276 (mmm) cc_final: 0.5068 (mmm) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.2397 time to fit residues: 172.9948 Evaluate side-chains 295 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN D 43 GLN D 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073066 restraints weight = 105610.399| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.37 r_work: 0.3139 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10700 Z= 0.179 Angle : 0.596 4.804 14452 Z= 0.336 Chirality : 0.036 0.145 1624 Planarity : 0.005 0.068 1756 Dihedral : 4.166 22.501 1408 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.67 % Favored : 93.69 % Rotamer: Outliers : 2.52 % Allowed : 11.20 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 1.32 (0.23), residues: 1252 helix: 1.28 (0.15), residues: 944 sheet: None (None), residues: 0 loop : -0.20 (0.42), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 75 TYR 0.011 0.001 TYR B 21 PHE 0.011 0.001 PHE D 252 TRP 0.005 0.001 TRP C 169 HIS 0.003 0.002 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00372 (10700) covalent geometry : angle 0.59617 (14452) hydrogen bonds : bond 0.06009 ( 760) hydrogen bonds : angle 4.57412 ( 2208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9440 (mp) cc_final: 0.9217 (mt) REVERT: A 221 ASP cc_start: 0.7874 (t0) cc_final: 0.7495 (m-30) REVERT: A 233 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8520 (mm-30) REVERT: B 221 ASP cc_start: 0.7864 (t0) cc_final: 0.7502 (m-30) REVERT: B 233 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8533 (mm-30) REVERT: B 269 ILE cc_start: 0.9177 (mt) cc_final: 0.8548 (mt) REVERT: C 233 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 302 ILE cc_start: 0.9782 (mt) cc_final: 0.9528 (mt) REVERT: D 204 TYR cc_start: 0.9193 (t80) cc_final: 0.8838 (t80) REVERT: D 233 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8557 (mm-30) outliers start: 29 outliers final: 15 residues processed: 384 average time/residue: 0.2047 time to fit residues: 114.1094 Evaluate side-chains 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 86 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 181 GLN C 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.084151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071271 restraints weight = 106388.523| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.30 r_work: 0.3107 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10700 Z= 0.166 Angle : 0.554 4.441 14452 Z= 0.306 Chirality : 0.035 0.135 1624 Planarity : 0.004 0.057 1756 Dihedral : 4.144 24.386 1408 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.35 % Favored : 94.01 % Rotamer: Outliers : 2.17 % Allowed : 12.59 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 1.72 (0.23), residues: 1252 helix: 1.71 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -0.83 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.012 0.001 TYR D 185 PHE 0.013 0.001 PHE B 252 TRP 0.006 0.001 TRP A 294 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00337 (10700) covalent geometry : angle 0.55409 (14452) hydrogen bonds : bond 0.04804 ( 760) hydrogen bonds : angle 4.34612 ( 2208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 338 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.8507 (pt0) cc_final: 0.8197 (pm20) REVERT: A 204 TYR cc_start: 0.9161 (t80) cc_final: 0.8930 (t80) REVERT: A 221 ASP cc_start: 0.8230 (t0) cc_final: 0.7931 (m-30) REVERT: A 233 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8516 (mm-30) REVERT: B 195 ARG cc_start: 0.8773 (mpt-90) cc_final: 0.8564 (mpt-90) REVERT: B 204 TYR cc_start: 0.9154 (t80) cc_final: 0.8918 (t80) REVERT: B 221 ASP cc_start: 0.8246 (t0) cc_final: 0.7946 (m-30) REVERT: B 233 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8530 (mm-30) REVERT: C 185 TYR cc_start: 0.9346 (t80) cc_final: 0.9100 (t80) REVERT: C 233 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8507 (mm-30) REVERT: D 195 ARG cc_start: 0.8796 (mpt-90) cc_final: 0.8593 (mpt-90) REVERT: D 204 TYR cc_start: 0.9285 (t80) cc_final: 0.8778 (t80) REVERT: D 233 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8552 (mm-30) outliers start: 25 outliers final: 17 residues processed: 340 average time/residue: 0.2050 time to fit residues: 100.1990 Evaluate side-chains 325 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 308 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.085552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.073285 restraints weight = 107717.000| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.31 r_work: 0.3143 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10700 Z= 0.144 Angle : 0.523 4.253 14452 Z= 0.289 Chirality : 0.034 0.130 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.112 25.000 1408 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.19 % Favored : 94.17 % Rotamer: Outliers : 2.26 % Allowed : 13.89 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 1.94 (0.24), residues: 1252 helix: 1.90 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 195 TYR 0.010 0.001 TYR D 185 PHE 0.009 0.001 PHE A 202 TRP 0.007 0.001 TRP D 294 HIS 0.000 0.000 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00295 (10700) covalent geometry : angle 0.52262 (14452) hydrogen bonds : bond 0.04408 ( 760) hydrogen bonds : angle 4.19484 ( 2208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8511 (tp40) REVERT: A 185 TYR cc_start: 0.9335 (t80) cc_final: 0.8971 (t80) REVERT: A 204 TYR cc_start: 0.9124 (t80) cc_final: 0.8903 (t80) REVERT: A 233 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8614 (mm-30) REVERT: A 241 MET cc_start: 0.9098 (mmp) cc_final: 0.8670 (mmp) REVERT: B 195 ARG cc_start: 0.8784 (mpt-90) cc_final: 0.8581 (mpt-90) REVERT: B 204 TYR cc_start: 0.9107 (t80) cc_final: 0.8866 (t80) REVERT: B 221 ASP cc_start: 0.8088 (t0) cc_final: 0.7888 (m-30) REVERT: B 233 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8657 (mm-30) REVERT: C 161 MET cc_start: 0.9566 (ttp) cc_final: 0.9282 (ptm) REVERT: C 204 TYR cc_start: 0.9134 (t80) cc_final: 0.8893 (t80) REVERT: C 233 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8677 (mm-30) REVERT: D 180 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8555 (tm-30) REVERT: D 185 TYR cc_start: 0.9319 (t80) cc_final: 0.8988 (t80) REVERT: D 204 TYR cc_start: 0.9250 (t80) cc_final: 0.8688 (t80) REVERT: D 233 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8645 (mm-30) outliers start: 26 outliers final: 16 residues processed: 336 average time/residue: 0.2004 time to fit residues: 98.4386 Evaluate side-chains 316 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.084480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072262 restraints weight = 108037.477| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.29 r_work: 0.3123 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10700 Z= 0.155 Angle : 0.520 4.510 14452 Z= 0.288 Chirality : 0.035 0.152 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.112 25.952 1408 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.99 % Favored : 93.61 % Rotamer: Outliers : 1.91 % Allowed : 15.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.14 (0.24), residues: 1252 helix: 2.02 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.011 0.001 TYR D 185 PHE 0.007 0.001 PHE D 252 TRP 0.008 0.001 TRP C 294 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00320 (10700) covalent geometry : angle 0.51994 (14452) hydrogen bonds : bond 0.04211 ( 760) hydrogen bonds : angle 4.11905 ( 2208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 311 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9584 (ttp) cc_final: 0.9312 (ptm) REVERT: A 185 TYR cc_start: 0.9308 (t80) cc_final: 0.9095 (t80) REVERT: A 204 TYR cc_start: 0.9191 (t80) cc_final: 0.8930 (t80) REVERT: A 233 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 241 MET cc_start: 0.9125 (mmp) cc_final: 0.8282 (mmp) REVERT: A 289 GLU cc_start: 0.8901 (tp30) cc_final: 0.8674 (tp30) REVERT: B 127 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7437 (t80) REVERT: B 204 TYR cc_start: 0.9200 (t80) cc_final: 0.8888 (t80) REVERT: B 221 ASP cc_start: 0.8092 (t0) cc_final: 0.7879 (m-30) REVERT: B 233 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8716 (mm-30) REVERT: B 241 MET cc_start: 0.9283 (mmm) cc_final: 0.8666 (mmm) REVERT: B 289 GLU cc_start: 0.8953 (tp30) cc_final: 0.8661 (tp30) REVERT: C 127 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7379 (t80) REVERT: C 185 TYR cc_start: 0.9303 (t80) cc_final: 0.9036 (t80) REVERT: C 204 TYR cc_start: 0.9205 (t80) cc_final: 0.8889 (t80) REVERT: C 233 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8724 (mm-30) REVERT: C 241 MET cc_start: 0.9298 (mmm) cc_final: 0.8889 (mmm) REVERT: D 127 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7437 (t80) REVERT: D 181 GLN cc_start: 0.8652 (pm20) cc_final: 0.8167 (mp10) REVERT: D 185 TYR cc_start: 0.9331 (t80) cc_final: 0.9011 (t80) REVERT: D 233 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8673 (mm-30) REVERT: D 279 MET cc_start: 0.9286 (mtp) cc_final: 0.9083 (mtp) outliers start: 22 outliers final: 16 residues processed: 313 average time/residue: 0.1960 time to fit residues: 90.2734 Evaluate side-chains 310 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.084047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071712 restraints weight = 108392.468| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.31 r_work: 0.3117 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10700 Z= 0.147 Angle : 0.503 4.190 14452 Z= 0.279 Chirality : 0.034 0.152 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.112 26.327 1408 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.31 % Favored : 93.37 % Rotamer: Outliers : 2.00 % Allowed : 16.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.24 (0.24), residues: 1252 helix: 2.13 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.009 0.001 TYR C 61 PHE 0.007 0.001 PHE D 211 TRP 0.008 0.001 TRP A 294 HIS 0.001 0.000 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00303 (10700) covalent geometry : angle 0.50314 (14452) hydrogen bonds : bond 0.04024 ( 760) hydrogen bonds : angle 4.01662 ( 2208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.9216 (t80) cc_final: 0.8888 (t80) REVERT: A 233 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8694 (mm-30) REVERT: A 241 MET cc_start: 0.9154 (mmp) cc_final: 0.8602 (mmp) REVERT: B 127 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7391 (t80) REVERT: B 185 TYR cc_start: 0.9263 (t80) cc_final: 0.9009 (t80) REVERT: B 204 TYR cc_start: 0.9213 (t80) cc_final: 0.8854 (t80) REVERT: B 233 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8715 (mm-30) REVERT: B 241 MET cc_start: 0.9258 (mmm) cc_final: 0.8766 (mmm) REVERT: B 289 GLU cc_start: 0.8980 (tp30) cc_final: 0.8614 (tp30) REVERT: C 114 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8837 (tm-30) REVERT: C 127 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7417 (t80) REVERT: C 161 MET cc_start: 0.9583 (ttp) cc_final: 0.9351 (ptm) REVERT: C 180 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8771 (tp40) REVERT: C 204 TYR cc_start: 0.9233 (t80) cc_final: 0.8877 (t80) REVERT: C 233 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8714 (mm-30) REVERT: D 127 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7398 (t80) REVERT: D 161 MET cc_start: 0.9608 (ttp) cc_final: 0.9392 (ptm) REVERT: D 185 TYR cc_start: 0.9306 (t80) cc_final: 0.8990 (t80) REVERT: D 190 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: D 233 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8696 (mm-30) REVERT: D 241 MET cc_start: 0.9070 (mmm) cc_final: 0.8650 (mmm) outliers start: 23 outliers final: 16 residues processed: 313 average time/residue: 0.2063 time to fit residues: 93.7255 Evaluate side-chains 312 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.082846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070361 restraints weight = 109512.516| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.25 r_work: 0.3097 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10700 Z= 0.183 Angle : 0.524 4.627 14452 Z= 0.291 Chirality : 0.035 0.156 1624 Planarity : 0.004 0.052 1756 Dihedral : 4.086 27.006 1408 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.47 % Favored : 93.21 % Rotamer: Outliers : 2.43 % Allowed : 18.40 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.29 (0.24), residues: 1252 helix: 2.19 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.010 0.001 TYR D 61 PHE 0.009 0.001 PHE B 211 TRP 0.005 0.001 TRP D 294 HIS 0.001 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00371 (10700) covalent geometry : angle 0.52433 (14452) hydrogen bonds : bond 0.04009 ( 760) hydrogen bonds : angle 4.07896 ( 2208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9590 (ttp) cc_final: 0.9372 (ptm) REVERT: A 170 THR cc_start: 0.9540 (m) cc_final: 0.9337 (p) REVERT: A 204 TYR cc_start: 0.9255 (t80) cc_final: 0.8801 (t80) REVERT: A 233 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8708 (mm-30) REVERT: B 43 GLN cc_start: 0.9456 (tp40) cc_final: 0.9103 (tp-100) REVERT: B 127 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 180 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8476 (tp40) REVERT: B 190 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8499 (tp30) REVERT: B 233 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8703 (mm-30) REVERT: C 127 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 170 THR cc_start: 0.9554 (m) cc_final: 0.9349 (p) REVERT: C 180 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8760 (tp40) REVERT: C 195 ARG cc_start: 0.8683 (mpt-90) cc_final: 0.8477 (mpt-90) REVERT: C 204 TYR cc_start: 0.9275 (t80) cc_final: 0.8849 (t80) REVERT: C 233 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8711 (mm-30) REVERT: D 43 GLN cc_start: 0.9448 (tp40) cc_final: 0.9096 (tp-100) REVERT: D 127 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7453 (t80) REVERT: D 233 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8688 (mm-30) outliers start: 28 outliers final: 14 residues processed: 309 average time/residue: 0.2011 time to fit residues: 89.7446 Evaluate side-chains 305 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 287 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.083398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071173 restraints weight = 108299.593| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.26 r_work: 0.3107 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10700 Z= 0.143 Angle : 0.522 4.268 14452 Z= 0.283 Chirality : 0.036 0.167 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.059 25.955 1408 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.39 % Favored : 93.29 % Rotamer: Outliers : 2.69 % Allowed : 18.75 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.33 (0.24), residues: 1252 helix: 2.22 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.014 0.001 TYR D 185 PHE 0.008 0.001 PHE D 211 TRP 0.005 0.001 TRP A 169 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00299 (10700) covalent geometry : angle 0.52217 (14452) hydrogen bonds : bond 0.03923 ( 760) hydrogen bonds : angle 3.98851 ( 2208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9599 (ttp) cc_final: 0.9350 (ptm) REVERT: A 204 TYR cc_start: 0.9193 (t80) cc_final: 0.8769 (t80) REVERT: A 233 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8690 (mm-30) REVERT: A 241 MET cc_start: 0.9139 (mmp) cc_final: 0.8648 (mmt) REVERT: B 43 GLN cc_start: 0.9442 (tp40) cc_final: 0.9096 (tp-100) REVERT: B 127 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 195 ARG cc_start: 0.8696 (mpt-90) cc_final: 0.8454 (mpt-90) REVERT: B 204 TYR cc_start: 0.9199 (t80) cc_final: 0.8825 (t80) REVERT: B 233 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8718 (mm-30) REVERT: C 114 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8803 (tm-30) REVERT: C 127 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7505 (t80) REVERT: C 170 THR cc_start: 0.9529 (m) cc_final: 0.9315 (p) REVERT: C 180 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8763 (tp40) REVERT: C 204 TYR cc_start: 0.9239 (t80) cc_final: 0.8826 (t80) REVERT: C 233 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8735 (mm-30) REVERT: D 43 GLN cc_start: 0.9448 (tp40) cc_final: 0.9111 (tp-100) REVERT: D 127 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7479 (t80) REVERT: D 233 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8696 (mm-30) outliers start: 31 outliers final: 18 residues processed: 301 average time/residue: 0.2098 time to fit residues: 92.2390 Evaluate side-chains 307 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.082730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070547 restraints weight = 110003.859| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.31 r_work: 0.3088 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10700 Z= 0.167 Angle : 0.531 4.756 14452 Z= 0.292 Chirality : 0.035 0.169 1624 Planarity : 0.004 0.052 1756 Dihedral : 4.076 26.451 1408 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 2.60 % Allowed : 18.75 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.29 (0.24), residues: 1252 helix: 2.15 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.010 0.001 TYR A 61 PHE 0.009 0.001 PHE B 211 TRP 0.003 0.001 TRP B 294 HIS 0.001 0.000 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00343 (10700) covalent geometry : angle 0.53127 (14452) hydrogen bonds : bond 0.03899 ( 760) hydrogen bonds : angle 4.01149 ( 2208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: A 233 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8705 (mm-30) REVERT: A 241 MET cc_start: 0.9161 (mmp) cc_final: 0.8706 (mmt) REVERT: B 43 GLN cc_start: 0.9460 (tp40) cc_final: 0.9118 (tp-100) REVERT: B 127 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 180 GLN cc_start: 0.8957 (tp40) cc_final: 0.8678 (tp40) REVERT: B 195 ARG cc_start: 0.8680 (mpt-90) cc_final: 0.8468 (mpt-90) REVERT: B 233 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8712 (mm-30) REVERT: C 127 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 170 THR cc_start: 0.9548 (m) cc_final: 0.9340 (p) REVERT: C 180 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8515 (tp40) REVERT: C 190 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: C 233 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8710 (mm-30) REVERT: D 43 GLN cc_start: 0.9463 (tp40) cc_final: 0.9134 (tp-100) REVERT: D 127 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7531 (t80) REVERT: D 190 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: D 233 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8691 (mm-30) outliers start: 30 outliers final: 15 residues processed: 297 average time/residue: 0.2214 time to fit residues: 96.3634 Evaluate side-chains 307 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 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 = 0.3486 r_free = 0.3486 target = 0.082502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070255 restraints weight = 110743.698| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.30 r_work: 0.3083 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10700 Z= 0.169 Angle : 0.574 8.791 14452 Z= 0.309 Chirality : 0.037 0.178 1624 Planarity : 0.004 0.052 1756 Dihedral : 4.104 26.055 1408 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 2.17 % Allowed : 20.14 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.20 (0.24), residues: 1252 helix: 2.08 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.009 0.001 TYR A 61 PHE 0.009 0.001 PHE B 211 TRP 0.009 0.001 TRP B 169 HIS 0.001 0.000 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00345 (10700) covalent geometry : angle 0.57395 (14452) hydrogen bonds : bond 0.03963 ( 760) hydrogen bonds : angle 4.00779 ( 2208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8523 (tm-30) REVERT: A 190 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: A 233 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8718 (mm-30) REVERT: A 241 MET cc_start: 0.9172 (mmp) cc_final: 0.8855 (mmt) REVERT: B 43 GLN cc_start: 0.9466 (tp40) cc_final: 0.9140 (tp-100) REVERT: B 127 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 190 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: B 233 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8699 (mm-30) REVERT: C 127 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 170 THR cc_start: 0.9528 (m) cc_final: 0.9326 (p) REVERT: C 180 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8520 (tp40) REVERT: C 190 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: C 233 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8731 (mm-30) REVERT: C 285 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9267 (mttt) REVERT: D 43 GLN cc_start: 0.9474 (tp40) cc_final: 0.9149 (tp-100) REVERT: D 127 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7478 (t80) REVERT: D 139 GLN cc_start: 0.9214 (tt0) cc_final: 0.8924 (tt0) REVERT: D 190 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: D 233 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8680 (mm-30) REVERT: D 257 ILE cc_start: 0.9819 (mm) cc_final: 0.9618 (pt) outliers start: 25 outliers final: 10 residues processed: 295 average time/residue: 0.2148 time to fit residues: 93.1571 Evaluate side-chains 302 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 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 = 0.3478 r_free = 0.3478 target = 0.081821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.069618 restraints weight = 110318.138| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.28 r_work: 0.3074 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10700 Z= 0.176 Angle : 0.561 6.768 14452 Z= 0.308 Chirality : 0.037 0.163 1624 Planarity : 0.004 0.052 1756 Dihedral : 4.092 26.231 1408 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 1.91 % Allowed : 20.49 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 2.16 (0.24), residues: 1252 helix: 2.08 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.010 0.001 TYR A 61 PHE 0.009 0.001 PHE A 211 TRP 0.007 0.001 TRP C 169 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00359 (10700) covalent geometry : angle 0.56090 (14452) hydrogen bonds : bond 0.03961 ( 760) hydrogen bonds : angle 4.01599 ( 2208) =============================================================================== Job complete usr+sys time: 4604.01 seconds wall clock time: 78 minutes 58.10 seconds (4738.10 seconds total)