Starting phenix.real_space_refine on Wed Feb 4 03:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkq_48334/02_2026/9mkq_48334.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5275 2.51 5 N 1535 2.21 5 O 1635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1701 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.39, per 1000 atoms: 0.16 Number of scatterers: 8505 At special positions: 0 Unit cell: (103.88, 99.64, 80.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1635 8.00 N 1535 7.00 C 5275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 212 " distance=2.06 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 212 " distance=2.06 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 212 " distance=2.06 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 212 " distance=2.06 Simple disulfide: pdb=" SG CYS E 188 " - pdb=" SG CYS E 212 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 399.6 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 76.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.543A pdb=" N PHE A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.832A pdb=" N THR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 63 through 85 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 168 through 184 removed outlier: 4.006A pdb=" N TYR A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.843A pdb=" N GLN A 201 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.543A pdb=" N PHE B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 3.832A pdb=" N THR B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 63 through 85 Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 168 through 184 removed outlier: 4.006A pdb=" N TYR B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.843A pdb=" N GLN B 201 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.543A pdb=" N PHE C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.833A pdb=" N THR C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 63 through 85 Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 168 through 184 removed outlier: 4.006A pdb=" N TYR C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.843A pdb=" N GLN C 201 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.543A pdb=" N PHE D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.833A pdb=" N THR D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 63 through 85 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 168 through 184 removed outlier: 4.006A pdb=" N TYR D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.843A pdb=" N GLN D 201 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.543A pdb=" N PHE E 20 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 46 removed outlier: 3.833A pdb=" N THR E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 63 through 85 Processing helix chain 'E' and resid 93 through 99 Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 150 through 165 Processing helix chain 'E' and resid 168 through 184 removed outlier: 4.006A pdb=" N TYR E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 197 through 202 removed outlier: 3.843A pdb=" N GLN E 201 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'E' and resid 2 through 4 575 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2945 1.35 - 1.47: 840 1.47 - 1.58: 4750 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 8640 Sorted by residual: bond pdb=" CG HIS C 135 " pdb=" CD2 HIS C 135 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.18e+01 bond pdb=" CG HIS E 135 " pdb=" CD2 HIS E 135 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.18e+01 bond pdb=" CG HIS A 135 " pdb=" CD2 HIS A 135 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.16e+01 bond pdb=" CG HIS D 135 " pdb=" CD2 HIS D 135 " ideal model delta sigma weight residual 1.354 1.317 0.037 1.10e-02 8.26e+03 1.16e+01 bond pdb=" CG HIS B 135 " pdb=" CD2 HIS B 135 " ideal model delta sigma weight residual 1.354 1.317 0.037 1.10e-02 8.26e+03 1.14e+01 ... (remaining 8635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 9521 2.24 - 4.47: 1977 4.47 - 6.71: 197 6.71 - 8.95: 5 8.95 - 11.19: 5 Bond angle restraints: 11705 Sorted by residual: angle pdb=" N ARG C 136 " pdb=" CA ARG C 136 " pdb=" C ARG C 136 " ideal model delta sigma weight residual 112.75 101.56 11.19 1.36e+00 5.41e-01 6.77e+01 angle pdb=" N ARG A 136 " pdb=" CA ARG A 136 " pdb=" C ARG A 136 " ideal model delta sigma weight residual 112.75 101.57 11.18 1.36e+00 5.41e-01 6.76e+01 angle pdb=" N ARG E 136 " pdb=" CA ARG E 136 " pdb=" C ARG E 136 " ideal model delta sigma weight residual 112.75 101.57 11.18 1.36e+00 5.41e-01 6.75e+01 angle pdb=" N ARG D 136 " pdb=" CA ARG D 136 " pdb=" C ARG D 136 " ideal model delta sigma weight residual 112.75 101.58 11.17 1.36e+00 5.41e-01 6.75e+01 angle pdb=" N ARG B 136 " pdb=" CA ARG B 136 " pdb=" C ARG B 136 " ideal model delta sigma weight residual 112.75 101.60 11.15 1.36e+00 5.41e-01 6.72e+01 ... (remaining 11700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.93: 5190 11.93 - 23.87: 75 23.87 - 35.80: 70 35.80 - 47.74: 5 47.74 - 59.67: 20 Dihedral angle restraints: 5360 sinusoidal: 2215 harmonic: 3145 Sorted by residual: dihedral pdb=" N HIS B 135 " pdb=" C HIS B 135 " pdb=" CA HIS B 135 " pdb=" CB HIS B 135 " ideal model delta harmonic sigma weight residual 122.80 131.69 -8.89 0 2.50e+00 1.60e-01 1.26e+01 dihedral pdb=" N HIS A 135 " pdb=" C HIS A 135 " pdb=" CA HIS A 135 " pdb=" CB HIS A 135 " ideal model delta harmonic sigma weight residual 122.80 131.67 -8.87 0 2.50e+00 1.60e-01 1.26e+01 dihedral pdb=" N HIS D 135 " pdb=" C HIS D 135 " pdb=" CA HIS D 135 " pdb=" CB HIS D 135 " ideal model delta harmonic sigma weight residual 122.80 131.66 -8.86 0 2.50e+00 1.60e-01 1.25e+01 ... (remaining 5357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 623 0.059 - 0.118: 408 0.118 - 0.177: 202 0.177 - 0.236: 81 0.236 - 0.295: 16 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA VAL B 167 " pdb=" N VAL B 167 " pdb=" C VAL B 167 " pdb=" CB VAL B 167 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA VAL D 167 " pdb=" N VAL D 167 " pdb=" C VAL D 167 " pdb=" CB VAL D 167 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA VAL E 167 " pdb=" N VAL E 167 " pdb=" C VAL E 167 " pdb=" CB VAL E 167 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1327 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 135 " 0.018 2.00e-02 2.50e+03 2.28e-02 7.76e+00 pdb=" CG HIS E 135 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS E 135 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS E 135 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS E 135 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 135 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 135 " -0.018 2.00e-02 2.50e+03 2.27e-02 7.76e+00 pdb=" CG HIS C 135 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS C 135 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS C 135 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS C 135 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 135 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 135 " 0.018 2.00e-02 2.50e+03 2.27e-02 7.74e+00 pdb=" CG HIS A 135 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS A 135 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS A 135 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 135 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 135 " -0.000 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 131 2.63 - 3.20: 9217 3.20 - 3.76: 13460 3.76 - 4.33: 19808 4.33 - 4.90: 29727 Nonbonded interactions: 72343 Sorted by model distance: nonbonded pdb=" OD1 ASP B 214 " pdb=" CG HIS C 135 " model vdw 2.060 3.260 nonbonded pdb=" OD1 ASP D 214 " pdb=" CG HIS E 135 " model vdw 2.060 3.260 nonbonded pdb=" CG HIS A 135 " pdb=" OD1 ASP E 214 " model vdw 2.060 3.260 nonbonded pdb=" OD1 ASP A 214 " pdb=" CG HIS B 135 " model vdw 2.060 3.260 nonbonded pdb=" OD1 ASP C 214 " pdb=" CG HIS D 135 " model vdw 2.060 3.260 ... (remaining 72338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.270 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 0.012 0.047 8645 Z= 0.894 Angle : 1.740 11.187 11715 Z= 1.353 Chirality : 0.098 0.295 1330 Planarity : 0.007 0.044 1535 Dihedral : 7.646 59.669 3295 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.53 % Allowed : 0.53 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1065 helix: 1.42 (0.20), residues: 700 sheet: 0.55 (0.64), residues: 45 loop : -0.65 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 64 TYR 0.017 0.003 TYR D 151 PHE 0.012 0.003 PHE D 154 TRP 0.035 0.008 TRP B 122 HIS 0.029 0.010 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.01210 ( 8640) covalent geometry : angle 1.73679 (11705) SS BOND : bond 0.02637 ( 5) SS BOND : angle 3.86524 ( 10) hydrogen bonds : bond 0.23395 ( 575) hydrogen bonds : angle 9.42792 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 401 time to evaluate : 0.392 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: A 13 LYS cc_start: 0.8631 (tttt) cc_final: 0.8220 (ttpp) REVERT: A 34 SER cc_start: 0.9195 (t) cc_final: 0.8842 (t) REVERT: A 183 ASN cc_start: 0.8963 (m-40) cc_final: 0.8630 (m-40) REVERT: B 13 LYS cc_start: 0.8574 (tttt) cc_final: 0.8215 (ttpp) REVERT: B 34 SER cc_start: 0.9273 (t) cc_final: 0.8716 (t) REVERT: B 53 ILE cc_start: 0.9336 (mt) cc_final: 0.9136 (mp) REVERT: C 13 LYS cc_start: 0.8676 (tttt) cc_final: 0.8328 (ttpp) REVERT: C 34 SER cc_start: 0.9288 (t) cc_final: 0.8910 (t) REVERT: C 38 GLU cc_start: 0.8038 (tt0) cc_final: 0.7791 (mt-10) REVERT: C 142 LEU cc_start: 0.8866 (mt) cc_final: 0.8594 (mt) REVERT: D 13 LYS cc_start: 0.8643 (tttt) cc_final: 0.8317 (ttpp) REVERT: D 34 SER cc_start: 0.9332 (t) cc_final: 0.8922 (t) REVERT: E 13 LYS cc_start: 0.8627 (tttt) cc_final: 0.8256 (ttpp) REVERT: E 34 SER cc_start: 0.9241 (t) cc_final: 0.8881 (t) REVERT: E 183 ASN cc_start: 0.8833 (m-40) cc_final: 0.8439 (m-40) outliers start: 5 outliers final: 0 residues processed: 406 average time/residue: 0.1349 time to fit residues: 68.2271 Evaluate side-chains 237 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 85 ASN A 114 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 114 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 114 GLN C 139 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 114 GLN D 191 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066137 restraints weight = 24215.306| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.31 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8645 Z= 0.193 Angle : 0.742 7.690 11715 Z= 0.403 Chirality : 0.041 0.123 1330 Planarity : 0.005 0.064 1535 Dihedral : 4.499 20.921 1160 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.35 % Allowed : 12.83 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1065 helix: 1.47 (0.18), residues: 745 sheet: -0.06 (0.62), residues: 45 loop : -0.32 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 80 TYR 0.025 0.003 TYR C 181 PHE 0.013 0.002 PHE A 20 TRP 0.026 0.003 TRP E 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8640) covalent geometry : angle 0.73252 (11705) SS BOND : bond 0.00436 ( 5) SS BOND : angle 4.21371 ( 10) hydrogen bonds : bond 0.06314 ( 575) hydrogen bonds : angle 6.26261 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7911 (tp30) cc_final: 0.7393 (tp30) REVERT: A 77 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8577 (tp30) REVERT: A 80 ARG cc_start: 0.9073 (ttm110) cc_final: 0.8792 (tmm160) REVERT: A 144 LYS cc_start: 0.8567 (mttm) cc_final: 0.8312 (mttp) REVERT: A 201 GLN cc_start: 0.8579 (mt0) cc_final: 0.8039 (mm-40) REVERT: A 206 GLU cc_start: 0.8566 (mp0) cc_final: 0.8232 (mp0) REVERT: B 34 SER cc_start: 0.8420 (t) cc_final: 0.8164 (t) REVERT: B 59 MET cc_start: 0.8968 (mtp) cc_final: 0.8415 (ttm) REVERT: B 60 MET cc_start: 0.8813 (mmp) cc_final: 0.8612 (mmm) REVERT: B 83 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8460 (ttp80) REVERT: B 84 GLN cc_start: 0.9073 (mt0) cc_final: 0.8766 (pt0) REVERT: B 85 ASN cc_start: 0.9500 (m-40) cc_final: 0.9236 (m-40) REVERT: B 144 LYS cc_start: 0.8333 (mttm) cc_final: 0.7597 (mmtp) REVERT: B 154 PHE cc_start: 0.7764 (t80) cc_final: 0.7003 (t80) REVERT: B 181 TYR cc_start: 0.8887 (t80) cc_final: 0.8639 (t80) REVERT: C 34 SER cc_start: 0.8489 (t) cc_final: 0.8079 (m) REVERT: C 73 LYS cc_start: 0.8809 (mptt) cc_final: 0.8427 (tppt) REVERT: C 80 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8635 (tmm160) REVERT: C 83 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8450 (ttp80) REVERT: C 179 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8068 (tp) REVERT: C 181 TYR cc_start: 0.8894 (t80) cc_final: 0.8396 (t80) REVERT: C 183 ASN cc_start: 0.8577 (m-40) cc_final: 0.8362 (m-40) REVERT: C 201 GLN cc_start: 0.8159 (mt0) cc_final: 0.7637 (mm-40) REVERT: D 34 SER cc_start: 0.8589 (t) cc_final: 0.8258 (m) REVERT: D 35 GLU cc_start: 0.8128 (tp30) cc_final: 0.7480 (tm-30) REVERT: D 77 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8593 (tp30) REVERT: D 80 ARG cc_start: 0.9343 (ttm110) cc_final: 0.8679 (ttp80) REVERT: D 84 GLN cc_start: 0.9167 (mt0) cc_final: 0.8732 (pt0) REVERT: D 142 LEU cc_start: 0.8904 (mt) cc_final: 0.8567 (pp) REVERT: D 183 ASN cc_start: 0.8478 (m110) cc_final: 0.7952 (m-40) REVERT: D 192 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8813 (mtp) REVERT: D 193 ASP cc_start: 0.8908 (m-30) cc_final: 0.8454 (m-30) REVERT: E 34 SER cc_start: 0.8329 (t) cc_final: 0.8002 (m) REVERT: E 80 ARG cc_start: 0.9375 (ttm110) cc_final: 0.8904 (tmm160) REVERT: E 113 ASP cc_start: 0.7635 (m-30) cc_final: 0.7275 (m-30) REVERT: E 183 ASN cc_start: 0.8827 (m-40) cc_final: 0.8620 (m-40) outliers start: 22 outliers final: 9 residues processed: 279 average time/residue: 0.1148 time to fit residues: 41.1844 Evaluate side-chains 222 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 132 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 139 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.064714 restraints weight = 24540.971| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.30 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8645 Z= 0.190 Angle : 0.675 6.730 11715 Z= 0.362 Chirality : 0.040 0.126 1330 Planarity : 0.004 0.043 1535 Dihedral : 4.397 18.464 1160 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.67 % Allowed : 15.40 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1065 helix: 1.60 (0.18), residues: 750 sheet: -0.33 (0.69), residues: 45 loop : -0.63 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.022 0.002 TYR A 181 PHE 0.009 0.002 PHE A 20 TRP 0.018 0.002 TRP E 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8640) covalent geometry : angle 0.67007 (11705) SS BOND : bond 0.00056 ( 5) SS BOND : angle 2.99797 ( 10) hydrogen bonds : bond 0.05531 ( 575) hydrogen bonds : angle 5.89254 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9085 (p0) cc_final: 0.8845 (p0) REVERT: A 112 MET cc_start: 0.8742 (mmm) cc_final: 0.8323 (mmm) REVERT: A 154 PHE cc_start: 0.8053 (t80) cc_final: 0.7687 (t80) REVERT: A 179 LEU cc_start: 0.8662 (tp) cc_final: 0.8460 (tp) REVERT: A 201 GLN cc_start: 0.8403 (mt0) cc_final: 0.7886 (mm-40) REVERT: A 204 THR cc_start: 0.8736 (p) cc_final: 0.8466 (p) REVERT: A 207 GLU cc_start: 0.8526 (mp0) cc_final: 0.8278 (pm20) REVERT: B 34 SER cc_start: 0.8741 (t) cc_final: 0.8254 (t) REVERT: B 59 MET cc_start: 0.9077 (mtp) cc_final: 0.8637 (ttm) REVERT: B 80 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.8888 (ttm110) REVERT: B 84 GLN cc_start: 0.9146 (mt0) cc_final: 0.8728 (pt0) REVERT: B 85 ASN cc_start: 0.9582 (m-40) cc_final: 0.9170 (m-40) REVERT: B 143 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7304 (p) REVERT: B 144 LYS cc_start: 0.8413 (mttm) cc_final: 0.7627 (mmtp) REVERT: B 154 PHE cc_start: 0.8045 (t80) cc_final: 0.7311 (t80) REVERT: B 181 TYR cc_start: 0.9028 (t80) cc_final: 0.8684 (t80) REVERT: B 183 ASN cc_start: 0.8610 (m-40) cc_final: 0.8215 (m-40) REVERT: B 201 GLN cc_start: 0.8553 (mt0) cc_final: 0.8071 (mm-40) REVERT: C 59 MET cc_start: 0.9078 (mtp) cc_final: 0.8770 (ttm) REVERT: C 112 MET cc_start: 0.9128 (mmm) cc_final: 0.8884 (mmm) REVERT: C 183 ASN cc_start: 0.8721 (m-40) cc_final: 0.8437 (m-40) REVERT: C 201 GLN cc_start: 0.8092 (mt0) cc_final: 0.7678 (mm-40) REVERT: C 204 THR cc_start: 0.8764 (p) cc_final: 0.8479 (p) REVERT: C 207 GLU cc_start: 0.8590 (mp0) cc_final: 0.8331 (pm20) REVERT: D 34 SER cc_start: 0.8816 (t) cc_final: 0.8377 (m) REVERT: D 59 MET cc_start: 0.8789 (mtp) cc_final: 0.8577 (ttm) REVERT: D 80 ARG cc_start: 0.9077 (ttm110) cc_final: 0.8664 (tmm160) REVERT: D 83 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8615 (ttp80) REVERT: D 84 GLN cc_start: 0.9304 (mt0) cc_final: 0.9081 (mm110) REVERT: D 142 LEU cc_start: 0.8963 (mt) cc_final: 0.8693 (pp) REVERT: D 193 ASP cc_start: 0.8948 (m-30) cc_final: 0.8340 (m-30) REVERT: D 201 GLN cc_start: 0.8184 (mt0) cc_final: 0.7933 (mm-40) REVERT: D 204 THR cc_start: 0.8702 (p) cc_final: 0.8489 (p) REVERT: D 207 GLU cc_start: 0.8797 (mp0) cc_final: 0.8574 (mp0) REVERT: E 34 SER cc_start: 0.8714 (t) cc_final: 0.8300 (m) REVERT: E 80 ARG cc_start: 0.9331 (ttm110) cc_final: 0.8975 (tmm160) REVERT: E 83 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8470 (ttp80) REVERT: E 85 ASN cc_start: 0.9486 (m-40) cc_final: 0.9247 (m-40) REVERT: E 144 LYS cc_start: 0.8772 (mttp) cc_final: 0.8079 (mmtp) REVERT: E 154 PHE cc_start: 0.7969 (t80) cc_final: 0.7746 (t80) REVERT: E 201 GLN cc_start: 0.8129 (mt0) cc_final: 0.7672 (mm-40) REVERT: E 207 GLU cc_start: 0.8478 (mp0) cc_final: 0.8194 (pm20) outliers start: 25 outliers final: 10 residues processed: 261 average time/residue: 0.1119 time to fit residues: 38.2384 Evaluate side-chains 225 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 132 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066276 restraints weight = 24696.651| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.30 r_work: 0.2856 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8645 Z= 0.151 Angle : 0.613 6.804 11715 Z= 0.326 Chirality : 0.039 0.128 1330 Planarity : 0.004 0.053 1535 Dihedral : 4.222 18.564 1160 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.46 % Allowed : 16.47 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1065 helix: 1.82 (0.18), residues: 730 sheet: 0.07 (0.71), residues: 45 loop : -0.72 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 83 TYR 0.022 0.002 TYR E 181 PHE 0.020 0.002 PHE C 154 TRP 0.018 0.002 TRP C 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8640) covalent geometry : angle 0.60858 (11705) SS BOND : bond 0.00151 ( 5) SS BOND : angle 2.49895 ( 10) hydrogen bonds : bond 0.04943 ( 575) hydrogen bonds : angle 5.62046 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9308 (ttp-110) cc_final: 0.8825 (mtm110) REVERT: A 152 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 201 GLN cc_start: 0.8415 (mt0) cc_final: 0.7946 (mm-40) REVERT: A 204 THR cc_start: 0.8748 (p) cc_final: 0.8509 (p) REVERT: A 207 GLU cc_start: 0.8755 (mp0) cc_final: 0.8505 (pm20) REVERT: B 34 SER cc_start: 0.8810 (t) cc_final: 0.8464 (m) REVERT: B 59 MET cc_start: 0.9194 (mtp) cc_final: 0.8779 (ttm) REVERT: B 80 ARG cc_start: 0.9159 (ttm-80) cc_final: 0.8798 (tmm160) REVERT: B 85 ASN cc_start: 0.9612 (m-40) cc_final: 0.9301 (m-40) REVERT: B 144 LYS cc_start: 0.8499 (mttm) cc_final: 0.7880 (mmtp) REVERT: B 154 PHE cc_start: 0.8178 (t80) cc_final: 0.7567 (t80) REVERT: B 181 TYR cc_start: 0.9101 (t80) cc_final: 0.8715 (t80) REVERT: B 183 ASN cc_start: 0.8692 (m-40) cc_final: 0.8151 (m-40) REVERT: B 192 MET cc_start: 0.9270 (mtm) cc_final: 0.9005 (mtt) REVERT: B 201 GLN cc_start: 0.7800 (mt0) cc_final: 0.7484 (mm-40) REVERT: C 34 SER cc_start: 0.8872 (t) cc_final: 0.8431 (m) REVERT: C 59 MET cc_start: 0.9144 (mtp) cc_final: 0.8667 (ttm) REVERT: C 183 ASN cc_start: 0.8927 (m-40) cc_final: 0.8678 (m-40) REVERT: C 201 GLN cc_start: 0.8089 (mt0) cc_final: 0.7656 (mm-40) REVERT: C 204 THR cc_start: 0.8755 (p) cc_final: 0.8487 (p) REVERT: C 207 GLU cc_start: 0.8770 (mp0) cc_final: 0.8441 (pm20) REVERT: D 34 SER cc_start: 0.8957 (t) cc_final: 0.8605 (m) REVERT: D 83 ARG cc_start: 0.8948 (ttp80) cc_final: 0.8717 (ttp80) REVERT: D 84 GLN cc_start: 0.9273 (mt0) cc_final: 0.8883 (pt0) REVERT: D 133 MET cc_start: 0.8898 (tmm) cc_final: 0.8630 (ppp) REVERT: D 142 LEU cc_start: 0.9094 (mt) cc_final: 0.8806 (pp) REVERT: D 204 THR cc_start: 0.8754 (p) cc_final: 0.8528 (p) REVERT: E 34 SER cc_start: 0.8902 (t) cc_final: 0.8523 (m) REVERT: E 80 ARG cc_start: 0.9331 (ttm110) cc_final: 0.8997 (ttp80) REVERT: E 83 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8731 (ttp80) REVERT: E 133 MET cc_start: 0.9235 (ttm) cc_final: 0.8801 (tmm) REVERT: E 144 LYS cc_start: 0.8865 (mttp) cc_final: 0.8190 (mmtp) REVERT: E 201 GLN cc_start: 0.8078 (mt0) cc_final: 0.7713 (mm-40) REVERT: E 207 GLU cc_start: 0.8852 (mp0) cc_final: 0.8591 (mp0) outliers start: 23 outliers final: 12 residues processed: 250 average time/residue: 0.0897 time to fit residues: 29.8669 Evaluate side-chains 227 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 98 optimal weight: 0.0060 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN D 24 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065652 restraints weight = 24484.079| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.49 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8645 Z= 0.190 Angle : 0.616 6.818 11715 Z= 0.325 Chirality : 0.039 0.203 1330 Planarity : 0.004 0.032 1535 Dihedral : 4.125 17.093 1160 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.99 % Allowed : 17.86 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1065 helix: 1.69 (0.18), residues: 755 sheet: None (None), residues: 0 loop : -0.39 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 83 TYR 0.030 0.002 TYR E 181 PHE 0.030 0.003 PHE D 154 TRP 0.009 0.001 TRP D 122 HIS 0.011 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8640) covalent geometry : angle 0.61293 (11705) SS BOND : bond 0.00294 ( 5) SS BOND : angle 2.27682 ( 10) hydrogen bonds : bond 0.04967 ( 575) hydrogen bonds : angle 5.44789 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9250 (ttp-110) cc_final: 0.8875 (ttp-110) REVERT: A 112 MET cc_start: 0.8851 (mmm) cc_final: 0.8273 (mmm) REVERT: A 199 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.8091 (mtm-85) REVERT: A 201 GLN cc_start: 0.8333 (mt0) cc_final: 0.7904 (mm-40) REVERT: A 204 THR cc_start: 0.8544 (p) cc_final: 0.8262 (p) REVERT: A 207 GLU cc_start: 0.8573 (mp0) cc_final: 0.8263 (pm20) REVERT: B 34 SER cc_start: 0.8758 (t) cc_final: 0.8353 (m) REVERT: B 59 MET cc_start: 0.8948 (mtp) cc_final: 0.8526 (ttm) REVERT: B 85 ASN cc_start: 0.9577 (m-40) cc_final: 0.9264 (m-40) REVERT: B 133 MET cc_start: 0.8429 (tmm) cc_final: 0.8185 (tmm) REVERT: B 144 LYS cc_start: 0.8475 (mttm) cc_final: 0.8014 (mmtp) REVERT: B 181 TYR cc_start: 0.9091 (t80) cc_final: 0.8701 (t80) REVERT: B 192 MET cc_start: 0.9142 (mtm) cc_final: 0.8908 (mtt) REVERT: B 201 GLN cc_start: 0.7672 (mt0) cc_final: 0.7407 (mm-40) REVERT: C 59 MET cc_start: 0.8946 (mtp) cc_final: 0.8502 (ttm) REVERT: C 83 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8546 (ttp80) REVERT: C 95 ASP cc_start: 0.9277 (t0) cc_final: 0.9056 (t0) REVERT: C 179 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8126 (tp) REVERT: C 201 GLN cc_start: 0.8043 (mt0) cc_final: 0.7767 (mm110) REVERT: C 207 GLU cc_start: 0.8534 (mp0) cc_final: 0.8189 (pm20) REVERT: D 34 SER cc_start: 0.8781 (t) cc_final: 0.8401 (m) REVERT: D 80 ARG cc_start: 0.9379 (ttm-80) cc_final: 0.8903 (tmm160) REVERT: D 84 GLN cc_start: 0.9225 (mt0) cc_final: 0.9018 (mm-40) REVERT: D 133 MET cc_start: 0.8695 (tmm) cc_final: 0.8452 (tmm) REVERT: D 142 LEU cc_start: 0.8966 (mt) cc_final: 0.8601 (pp) REVERT: D 154 PHE cc_start: 0.7775 (t80) cc_final: 0.7491 (t80) REVERT: D 182 THR cc_start: 0.9080 (m) cc_final: 0.8809 (p) REVERT: E 34 SER cc_start: 0.8743 (t) cc_final: 0.8338 (m) REVERT: E 80 ARG cc_start: 0.9227 (ttm110) cc_final: 0.8958 (ttp80) REVERT: E 83 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8660 (ttp80) REVERT: E 133 MET cc_start: 0.9092 (ttm) cc_final: 0.8623 (tmm) REVERT: E 179 LEU cc_start: 0.8711 (tp) cc_final: 0.8408 (tp) REVERT: E 201 GLN cc_start: 0.8051 (mt0) cc_final: 0.7612 (mm-40) REVERT: E 207 GLU cc_start: 0.8599 (mp0) cc_final: 0.8355 (mp0) outliers start: 28 outliers final: 14 residues processed: 243 average time/residue: 0.0921 time to fit residues: 29.8076 Evaluate side-chains 227 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064601 restraints weight = 24734.313| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.23 r_work: 0.2821 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8645 Z= 0.192 Angle : 0.617 6.933 11715 Z= 0.326 Chirality : 0.039 0.131 1330 Planarity : 0.004 0.039 1535 Dihedral : 4.117 16.868 1160 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.78 % Allowed : 18.82 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1065 helix: 1.83 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.32 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 83 TYR 0.019 0.002 TYR A 181 PHE 0.024 0.004 PHE C 154 TRP 0.008 0.001 TRP D 122 HIS 0.011 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8640) covalent geometry : angle 0.61358 (11705) SS BOND : bond 0.00295 ( 5) SS BOND : angle 2.30272 ( 10) hydrogen bonds : bond 0.04840 ( 575) hydrogen bonds : angle 5.34963 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9349 (ttp-110) cc_final: 0.8965 (ttp-110) REVERT: A 112 MET cc_start: 0.9145 (mmm) cc_final: 0.8570 (mmm) REVERT: A 152 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 199 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: A 201 GLN cc_start: 0.8447 (mt0) cc_final: 0.7970 (mm-40) REVERT: A 207 GLU cc_start: 0.8829 (mp0) cc_final: 0.8564 (pm20) REVERT: B 34 SER cc_start: 0.9078 (t) cc_final: 0.8717 (m) REVERT: B 59 MET cc_start: 0.9229 (mtp) cc_final: 0.8899 (ttm) REVERT: B 85 ASN cc_start: 0.9640 (m-40) cc_final: 0.9350 (m-40) REVERT: B 133 MET cc_start: 0.8812 (tmm) cc_final: 0.8576 (tmm) REVERT: B 143 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 144 LYS cc_start: 0.8736 (mttm) cc_final: 0.8055 (mmtp) REVERT: B 154 PHE cc_start: 0.8363 (t80) cc_final: 0.7747 (t80) REVERT: B 181 TYR cc_start: 0.9202 (t80) cc_final: 0.8939 (t80) REVERT: B 183 ASN cc_start: 0.8870 (m-40) cc_final: 0.8648 (m-40) REVERT: C 59 MET cc_start: 0.9238 (mtp) cc_final: 0.8861 (ttm) REVERT: C 95 ASP cc_start: 0.9354 (t0) cc_final: 0.9141 (t0) REVERT: C 144 LYS cc_start: 0.9269 (mttp) cc_final: 0.9063 (mmtm) REVERT: C 172 LYS cc_start: 0.8442 (mttt) cc_final: 0.8221 (mttm) REVERT: C 179 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8372 (tp) REVERT: C 181 TYR cc_start: 0.9187 (t80) cc_final: 0.8834 (t80) REVERT: C 182 THR cc_start: 0.9119 (p) cc_final: 0.8870 (p) REVERT: C 201 GLN cc_start: 0.7976 (mt0) cc_final: 0.7688 (mm-40) REVERT: D 34 SER cc_start: 0.9083 (t) cc_final: 0.8824 (m) REVERT: D 80 ARG cc_start: 0.9482 (ttm-80) cc_final: 0.8883 (tmm160) REVERT: D 84 GLN cc_start: 0.9289 (mt0) cc_final: 0.8984 (tt0) REVERT: D 133 MET cc_start: 0.9061 (tmm) cc_final: 0.8761 (tmm) REVERT: D 142 LEU cc_start: 0.9073 (mt) cc_final: 0.8701 (pp) REVERT: D 154 PHE cc_start: 0.8321 (t80) cc_final: 0.7997 (t80) REVERT: D 194 ARG cc_start: 0.2671 (tpt170) cc_final: 0.0435 (ttt-90) REVERT: D 199 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8433 (mtm-85) REVERT: E 34 SER cc_start: 0.9131 (t) cc_final: 0.8784 (m) REVERT: E 80 ARG cc_start: 0.9311 (ttm110) cc_final: 0.9057 (ttp80) REVERT: E 133 MET cc_start: 0.9280 (ttm) cc_final: 0.8895 (tmm) REVERT: E 201 GLN cc_start: 0.8171 (mt0) cc_final: 0.7741 (mm-40) REVERT: E 207 GLU cc_start: 0.8838 (mp0) cc_final: 0.8549 (mp0) outliers start: 26 outliers final: 16 residues processed: 238 average time/residue: 0.0939 time to fit residues: 29.7068 Evaluate side-chains 223 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 28 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065882 restraints weight = 25096.525| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.29 r_work: 0.2860 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8645 Z= 0.150 Angle : 0.616 7.042 11715 Z= 0.323 Chirality : 0.040 0.309 1330 Planarity : 0.004 0.028 1535 Dihedral : 4.045 16.309 1160 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.57 % Allowed : 19.68 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1065 helix: 1.90 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.35 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 83 TYR 0.021 0.002 TYR E 181 PHE 0.026 0.003 PHE C 154 TRP 0.009 0.001 TRP E 81 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8640) covalent geometry : angle 0.61142 (11705) SS BOND : bond 0.00188 ( 5) SS BOND : angle 2.54201 ( 10) hydrogen bonds : bond 0.04576 ( 575) hydrogen bonds : angle 5.25494 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9362 (ttp-110) cc_final: 0.8948 (ttp-110) REVERT: A 144 LYS cc_start: 0.9258 (mmtp) cc_final: 0.8910 (mmtm) REVERT: A 201 GLN cc_start: 0.8323 (mt0) cc_final: 0.7947 (mm-40) REVERT: A 207 GLU cc_start: 0.8876 (mp0) cc_final: 0.8600 (pm20) REVERT: B 34 SER cc_start: 0.9025 (t) cc_final: 0.8704 (m) REVERT: B 59 MET cc_start: 0.9149 (mtp) cc_final: 0.8874 (ttm) REVERT: B 85 ASN cc_start: 0.9646 (m-40) cc_final: 0.9371 (m-40) REVERT: B 133 MET cc_start: 0.8837 (tmm) cc_final: 0.8446 (tmm) REVERT: B 144 LYS cc_start: 0.8754 (mttm) cc_final: 0.8061 (mmtp) REVERT: B 154 PHE cc_start: 0.8315 (t80) cc_final: 0.7802 (t80) REVERT: B 181 TYR cc_start: 0.9192 (t80) cc_final: 0.8883 (t80) REVERT: B 183 ASN cc_start: 0.8890 (m-40) cc_final: 0.8637 (m-40) REVERT: B 199 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: C 59 MET cc_start: 0.9157 (mtp) cc_final: 0.8873 (ttm) REVERT: C 95 ASP cc_start: 0.9369 (t0) cc_final: 0.9143 (t0) REVERT: C 179 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 181 TYR cc_start: 0.9204 (t80) cc_final: 0.8893 (t80) REVERT: C 194 ARG cc_start: 0.2536 (tpt170) cc_final: 0.0788 (ttt-90) REVERT: C 199 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8367 (mtm110) REVERT: D 34 SER cc_start: 0.9059 (t) cc_final: 0.8771 (m) REVERT: D 80 ARG cc_start: 0.9365 (ttm-80) cc_final: 0.8954 (tmm160) REVERT: D 133 MET cc_start: 0.9078 (tmm) cc_final: 0.8749 (tmm) REVERT: D 142 LEU cc_start: 0.9083 (mt) cc_final: 0.8725 (pp) REVERT: D 154 PHE cc_start: 0.8308 (t80) cc_final: 0.8009 (t80) REVERT: D 194 ARG cc_start: 0.2715 (tpt170) cc_final: 0.0360 (ttt-90) REVERT: E 34 SER cc_start: 0.9057 (t) cc_final: 0.8722 (m) REVERT: E 80 ARG cc_start: 0.9294 (ttm110) cc_final: 0.9034 (ttp80) REVERT: E 83 ARG cc_start: 0.9217 (ttp-110) cc_final: 0.8758 (ttp80) REVERT: E 133 MET cc_start: 0.9233 (ttm) cc_final: 0.8823 (tmm) REVERT: E 144 LYS cc_start: 0.9191 (mttm) cc_final: 0.8529 (mmtm) REVERT: E 194 ARG cc_start: 0.2605 (tpt170) cc_final: 0.0446 (ttt-90) REVERT: E 207 GLU cc_start: 0.8861 (mp0) cc_final: 0.8534 (mp0) outliers start: 24 outliers final: 14 residues processed: 230 average time/residue: 0.0967 time to fit residues: 29.4321 Evaluate side-chains 216 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN D 183 ASN E 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.084746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064691 restraints weight = 24636.216| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.33 r_work: 0.2856 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8645 Z= 0.168 Angle : 0.619 8.049 11715 Z= 0.324 Chirality : 0.039 0.154 1330 Planarity : 0.004 0.029 1535 Dihedral : 3.996 16.517 1160 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.57 % Allowed : 20.32 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1065 helix: 1.92 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.23 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.039 0.002 TYR A 181 PHE 0.029 0.004 PHE C 154 TRP 0.008 0.001 TRP D 122 HIS 0.011 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8640) covalent geometry : angle 0.61452 (11705) SS BOND : bond 0.00252 ( 5) SS BOND : angle 2.52916 ( 10) hydrogen bonds : bond 0.04577 ( 575) hydrogen bonds : angle 5.13606 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.368 Fit side-chains REVERT: A 83 ARG cc_start: 0.9371 (ttp-110) cc_final: 0.8896 (ttp-110) REVERT: A 144 LYS cc_start: 0.9337 (mmtp) cc_final: 0.8924 (mmtm) REVERT: A 154 PHE cc_start: 0.8248 (t80) cc_final: 0.7743 (t80) REVERT: A 201 GLN cc_start: 0.8335 (mt0) cc_final: 0.8055 (mm-40) REVERT: A 202 GLN cc_start: 0.8112 (mp10) cc_final: 0.7689 (mp10) REVERT: A 207 GLU cc_start: 0.8872 (mp0) cc_final: 0.8606 (mp0) REVERT: B 34 SER cc_start: 0.9049 (t) cc_final: 0.8729 (m) REVERT: B 85 ASN cc_start: 0.9637 (m-40) cc_final: 0.9359 (m-40) REVERT: B 133 MET cc_start: 0.8937 (tmm) cc_final: 0.8584 (tmm) REVERT: B 144 LYS cc_start: 0.8832 (mttm) cc_final: 0.8198 (mmtp) REVERT: B 181 TYR cc_start: 0.9229 (t80) cc_final: 0.8900 (t80) REVERT: B 192 MET cc_start: 0.9147 (mmt) cc_final: 0.8495 (mmt) REVERT: B 202 GLN cc_start: 0.8040 (mp10) cc_final: 0.7617 (mp10) REVERT: C 59 MET cc_start: 0.9163 (mtp) cc_final: 0.8793 (ttm) REVERT: C 95 ASP cc_start: 0.9359 (t0) cc_final: 0.9139 (t0) REVERT: C 142 LEU cc_start: 0.9148 (mt) cc_final: 0.8885 (pp) REVERT: C 179 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8288 (tt) REVERT: C 181 TYR cc_start: 0.9190 (t80) cc_final: 0.8859 (t80) REVERT: C 194 ARG cc_start: 0.2491 (tpt170) cc_final: 0.0547 (ttt-90) REVERT: C 199 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8327 (mtm-85) REVERT: D 34 SER cc_start: 0.9094 (t) cc_final: 0.8801 (m) REVERT: D 80 ARG cc_start: 0.9326 (ttm-80) cc_final: 0.8879 (tmm160) REVERT: D 84 GLN cc_start: 0.9306 (mm-40) cc_final: 0.9089 (mm-40) REVERT: D 133 MET cc_start: 0.9098 (tmm) cc_final: 0.8759 (tmm) REVERT: D 142 LEU cc_start: 0.9171 (mt) cc_final: 0.8798 (pp) REVERT: D 144 LYS cc_start: 0.9310 (mttp) cc_final: 0.8411 (mmtp) REVERT: D 194 ARG cc_start: 0.2443 (tpt170) cc_final: 0.0225 (ttt-90) REVERT: E 34 SER cc_start: 0.9100 (t) cc_final: 0.8772 (m) REVERT: E 80 ARG cc_start: 0.9285 (ttm110) cc_final: 0.9036 (ttp80) REVERT: E 83 ARG cc_start: 0.9200 (ttp-110) cc_final: 0.8896 (ttp80) REVERT: E 95 ASP cc_start: 0.9508 (t0) cc_final: 0.9293 (t0) REVERT: E 133 MET cc_start: 0.9253 (ttm) cc_final: 0.8868 (tmm) REVERT: E 144 LYS cc_start: 0.9215 (mttm) cc_final: 0.8532 (mmtm) REVERT: E 194 ARG cc_start: 0.2583 (tpt170) cc_final: 0.0494 (ttt-90) REVERT: E 207 GLU cc_start: 0.8851 (mp0) cc_final: 0.8511 (mp0) REVERT: E 209 MET cc_start: 0.8654 (tpt) cc_final: 0.8385 (tpt) outliers start: 24 outliers final: 16 residues processed: 224 average time/residue: 0.1064 time to fit residues: 31.3901 Evaluate side-chains 220 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.086642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066616 restraints weight = 24457.431| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.34 r_work: 0.2893 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8645 Z= 0.136 Angle : 0.609 7.924 11715 Z= 0.318 Chirality : 0.039 0.163 1330 Planarity : 0.004 0.028 1535 Dihedral : 3.950 16.739 1160 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.93 % Allowed : 21.28 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1065 helix: 1.88 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.03 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 83 TYR 0.027 0.002 TYR A 181 PHE 0.031 0.003 PHE C 154 TRP 0.009 0.001 TRP D 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8640) covalent geometry : angle 0.60452 (11705) SS BOND : bond 0.00296 ( 5) SS BOND : angle 2.58665 ( 10) hydrogen bonds : bond 0.04301 ( 575) hydrogen bonds : angle 5.07610 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.8969 (ttp-110) REVERT: A 144 LYS cc_start: 0.9433 (mmtp) cc_final: 0.9025 (mmtm) REVERT: A 154 PHE cc_start: 0.8223 (t80) cc_final: 0.7778 (t80) REVERT: A 202 GLN cc_start: 0.8238 (mp10) cc_final: 0.7837 (mp10) REVERT: A 207 GLU cc_start: 0.8865 (mp0) cc_final: 0.8591 (mp0) REVERT: B 34 SER cc_start: 0.8990 (t) cc_final: 0.8707 (m) REVERT: B 85 ASN cc_start: 0.9654 (m-40) cc_final: 0.9209 (m-40) REVERT: B 112 MET cc_start: 0.9002 (mmm) cc_final: 0.8670 (mmm) REVERT: B 133 MET cc_start: 0.8939 (tmm) cc_final: 0.8573 (tmm) REVERT: B 143 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 144 LYS cc_start: 0.8974 (mttm) cc_final: 0.8326 (mmtp) REVERT: B 154 PHE cc_start: 0.8275 (t80) cc_final: 0.7559 (t80) REVERT: B 181 TYR cc_start: 0.9194 (t80) cc_final: 0.8817 (t80) REVERT: B 192 MET cc_start: 0.9186 (mmt) cc_final: 0.8602 (mmt) REVERT: B 202 GLN cc_start: 0.8022 (mp10) cc_final: 0.7540 (mp10) REVERT: C 59 MET cc_start: 0.9069 (mtp) cc_final: 0.8733 (ttm) REVERT: C 95 ASP cc_start: 0.9352 (t0) cc_final: 0.9122 (t0) REVERT: C 142 LEU cc_start: 0.9153 (mt) cc_final: 0.8888 (pp) REVERT: C 179 LEU cc_start: 0.8700 (tp) cc_final: 0.8246 (tp) REVERT: C 181 TYR cc_start: 0.9183 (t80) cc_final: 0.8805 (t80) REVERT: C 192 MET cc_start: 0.9422 (mmm) cc_final: 0.9185 (mmm) REVERT: C 194 ARG cc_start: 0.2227 (tpt170) cc_final: 0.0367 (ttt-90) REVERT: C 199 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8478 (mtm-85) REVERT: C 202 GLN cc_start: 0.8083 (mp10) cc_final: 0.7690 (mp10) REVERT: D 28 MET cc_start: 0.9235 (tpp) cc_final: 0.9022 (tpp) REVERT: D 34 SER cc_start: 0.9069 (t) cc_final: 0.8739 (m) REVERT: D 80 ARG cc_start: 0.9311 (ttm-80) cc_final: 0.8879 (tmm160) REVERT: D 84 GLN cc_start: 0.9278 (mm-40) cc_final: 0.9060 (mm-40) REVERT: D 133 MET cc_start: 0.9001 (tmm) cc_final: 0.8660 (tmm) REVERT: D 142 LEU cc_start: 0.9172 (mt) cc_final: 0.8794 (pp) REVERT: D 144 LYS cc_start: 0.9293 (mttp) cc_final: 0.8526 (mmtp) REVERT: D 194 ARG cc_start: 0.2616 (tpt170) cc_final: 0.0537 (ttt-90) REVERT: D 202 GLN cc_start: 0.8211 (mp10) cc_final: 0.7805 (mp10) REVERT: E 34 SER cc_start: 0.9002 (t) cc_final: 0.8671 (m) REVERT: E 59 MET cc_start: 0.8780 (mtp) cc_final: 0.8567 (ttm) REVERT: E 80 ARG cc_start: 0.9267 (ttm110) cc_final: 0.9037 (ttp80) REVERT: E 83 ARG cc_start: 0.9238 (ttp-110) cc_final: 0.8947 (ttp80) REVERT: E 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9307 (t0) REVERT: E 133 MET cc_start: 0.9195 (ttm) cc_final: 0.8862 (tmm) REVERT: E 154 PHE cc_start: 0.8258 (t80) cc_final: 0.7927 (t80) REVERT: E 157 ARG cc_start: 0.8948 (mtm-85) cc_final: 0.8740 (mtm-85) REVERT: E 182 THR cc_start: 0.9311 (m) cc_final: 0.8995 (p) REVERT: E 194 ARG cc_start: 0.2567 (tpt170) cc_final: 0.0614 (ttt-90) REVERT: E 207 GLU cc_start: 0.8781 (mp0) cc_final: 0.8454 (mp0) REVERT: E 208 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8623 (mmtm) outliers start: 18 outliers final: 13 residues processed: 234 average time/residue: 0.1174 time to fit residues: 35.6897 Evaluate side-chains 217 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065770 restraints weight = 24497.491| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.35 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8645 Z= 0.154 Angle : 0.621 7.804 11715 Z= 0.321 Chirality : 0.039 0.155 1330 Planarity : 0.004 0.028 1535 Dihedral : 3.935 21.761 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.71 % Allowed : 21.93 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1065 helix: 1.90 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.05 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 64 TYR 0.037 0.002 TYR E 181 PHE 0.030 0.003 PHE C 154 TRP 0.008 0.001 TRP D 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8640) covalent geometry : angle 0.61653 (11705) SS BOND : bond 0.00220 ( 5) SS BOND : angle 2.47951 ( 10) hydrogen bonds : bond 0.04366 ( 575) hydrogen bonds : angle 5.02564 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.355 Fit side-chains REVERT: A 83 ARG cc_start: 0.9358 (ttp-110) cc_final: 0.8834 (ttp-110) REVERT: A 95 ASP cc_start: 0.9422 (t0) cc_final: 0.9190 (t0) REVERT: A 144 LYS cc_start: 0.9443 (mmtp) cc_final: 0.9085 (mmtp) REVERT: A 202 GLN cc_start: 0.8122 (mp10) cc_final: 0.7596 (mp10) REVERT: A 207 GLU cc_start: 0.8629 (mp0) cc_final: 0.8370 (mp0) REVERT: B 34 SER cc_start: 0.8957 (t) cc_final: 0.8631 (m) REVERT: B 85 ASN cc_start: 0.9598 (m-40) cc_final: 0.9354 (m-40) REVERT: B 112 MET cc_start: 0.8858 (mmm) cc_final: 0.8471 (mmm) REVERT: B 133 MET cc_start: 0.8706 (tmm) cc_final: 0.8333 (tmm) REVERT: B 144 LYS cc_start: 0.8958 (mttm) cc_final: 0.8345 (mmtp) REVERT: B 154 PHE cc_start: 0.8351 (t80) cc_final: 0.7642 (t80) REVERT: B 181 TYR cc_start: 0.9199 (t80) cc_final: 0.8804 (t80) REVERT: B 192 MET cc_start: 0.9181 (mmt) cc_final: 0.8881 (mmt) REVERT: B 202 GLN cc_start: 0.7866 (mp10) cc_final: 0.7448 (mp10) REVERT: C 59 MET cc_start: 0.8812 (mtp) cc_final: 0.8395 (ttm) REVERT: C 95 ASP cc_start: 0.9272 (t0) cc_final: 0.9022 (t0) REVERT: C 179 LEU cc_start: 0.8715 (tp) cc_final: 0.8264 (tt) REVERT: C 181 TYR cc_start: 0.9153 (t80) cc_final: 0.8667 (t80) REVERT: C 194 ARG cc_start: 0.1962 (tpt170) cc_final: 0.0455 (ttt-90) REVERT: C 199 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8401 (mtm-85) REVERT: C 202 GLN cc_start: 0.7944 (mp10) cc_final: 0.7633 (mp10) REVERT: D 34 SER cc_start: 0.8978 (t) cc_final: 0.8614 (m) REVERT: D 80 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8808 (tmm160) REVERT: D 84 GLN cc_start: 0.9227 (mm-40) cc_final: 0.9005 (mm-40) REVERT: D 133 MET cc_start: 0.8827 (tmm) cc_final: 0.8468 (tmm) REVERT: D 142 LEU cc_start: 0.9162 (mt) cc_final: 0.8740 (pp) REVERT: D 144 LYS cc_start: 0.9315 (mttp) cc_final: 0.8474 (mmtp) REVERT: D 194 ARG cc_start: 0.2066 (tpt170) cc_final: 0.0603 (ttt-90) REVERT: E 34 SER cc_start: 0.8900 (t) cc_final: 0.8583 (m) REVERT: E 83 ARG cc_start: 0.9175 (ttp-110) cc_final: 0.8877 (ttp80) REVERT: E 95 ASP cc_start: 0.9441 (t0) cc_final: 0.9204 (t0) REVERT: E 133 MET cc_start: 0.9016 (ttm) cc_final: 0.8722 (tmm) REVERT: E 144 LYS cc_start: 0.9291 (mttm) cc_final: 0.8510 (mmtm) REVERT: E 157 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8583 (mtm-85) REVERT: E 182 THR cc_start: 0.9238 (m) cc_final: 0.8949 (p) REVERT: E 194 ARG cc_start: 0.2001 (tpt170) cc_final: 0.0616 (ttt-90) REVERT: E 207 GLU cc_start: 0.8524 (mp0) cc_final: 0.8162 (mp0) REVERT: E 209 MET cc_start: 0.8475 (tpt) cc_final: 0.8158 (tpt) outliers start: 16 outliers final: 14 residues processed: 225 average time/residue: 0.1206 time to fit residues: 35.3016 Evaluate side-chains 211 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065286 restraints weight = 24518.754| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.33 r_work: 0.2838 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8645 Z= 0.171 Angle : 0.638 7.917 11715 Z= 0.330 Chirality : 0.039 0.140 1330 Planarity : 0.004 0.046 1535 Dihedral : 3.974 21.428 1160 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.60 % Allowed : 22.67 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1065 helix: 1.87 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.06 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 80 TYR 0.034 0.002 TYR E 181 PHE 0.030 0.003 PHE C 154 TRP 0.008 0.001 TRP D 122 HIS 0.011 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8640) covalent geometry : angle 0.63407 (11705) SS BOND : bond 0.00246 ( 5) SS BOND : angle 2.43568 ( 10) hydrogen bonds : bond 0.04423 ( 575) hydrogen bonds : angle 5.01810 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.23 seconds wall clock time: 29 minutes 53.43 seconds (1793.43 seconds total)