Starting phenix.real_space_refine on Thu Sep 18 03:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynn_39428/09_2025/8ynn_39428.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic. 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 58 5.16 5 C 6425 2.51 5 N 1731 2.21 5 O 1905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10119 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "H" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1393 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain breaks: 1 Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 10119 At special positions: 0 Unit cell: (102.48, 100.8, 122.64, 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 58 16.00 O 1905 8.00 N 1731 7.00 C 6425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 412.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.992A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.756A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.007A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.564A pdb=" N MET B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.519A pdb=" N VAL B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.769A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.564A pdb=" N LEU C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.586A pdb=" N ILE C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 47 Processing helix chain 'H' and resid 51 through 61 removed outlier: 3.688A pdb=" N GLU H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 75 through 86 removed outlier: 4.313A pdb=" N VAL H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 149 through 159 removed outlier: 3.517A pdb=" N ILE H 159 " --> pdb=" O CYS H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 175 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.715A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 176 removed outlier: 3.946A pdb=" N LYS I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 14 through 26 Processing helix chain 'J' and resid 36 through 47 Processing helix chain 'J' and resid 51 through 62 removed outlier: 3.529A pdb=" N VAL J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 71 removed outlier: 4.128A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 removed outlier: 3.636A pdb=" N VAL J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 103 removed outlier: 3.542A pdb=" N VAL J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 117 removed outlier: 3.519A pdb=" N VAL J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 120 No H-bonds generated for 'chain 'J' and resid 118 through 120' Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.969A pdb=" N LYS J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.666A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.724A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 51 through 63 Processing helix chain 'K' and resid 64 through 71 removed outlier: 3.681A pdb=" N LEU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.884A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 4.313A pdb=" N LYS K 127 " --> pdb=" O GLY K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 579 hydrogen bonds defined for protein. 1737 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: 1.60 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3387 1.34 - 1.46: 1863 1.46 - 1.58: 4872 1.58 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 10224 Sorted by residual: bond pdb=" C GLU C 36 " pdb=" N PRO C 37 " ideal model delta sigma weight residual 1.334 1.346 -0.012 8.40e-03 1.42e+04 2.02e+00 bond pdb=" CA VAL J 33 " pdb=" C VAL J 33 " ideal model delta sigma weight residual 1.528 1.535 -0.007 7.70e-03 1.69e+04 8.39e-01 bond pdb=" C GLU A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 1.331 1.337 -0.006 7.90e-03 1.60e+04 5.09e-01 bond pdb=" CA VAL A 150 " pdb=" CB VAL A 150 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.74e-01 bond pdb=" N ILE C 30 " pdb=" CA ILE C 30 " ideal model delta sigma weight residual 1.461 1.453 0.008 1.23e-02 6.61e+03 4.68e-01 ... (remaining 10219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 13153 0.93 - 1.85: 434 1.85 - 2.78: 78 2.78 - 3.70: 18 3.70 - 4.63: 10 Bond angle restraints: 13693 Sorted by residual: angle pdb=" C ARG A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 121.97 126.60 -4.63 1.80e+00 3.09e-01 6.61e+00 angle pdb=" C ARG C 149 " pdb=" N VAL C 150 " pdb=" CA VAL C 150 " ideal model delta sigma weight residual 121.97 126.51 -4.54 1.80e+00 3.09e-01 6.37e+00 angle pdb=" C ARG B 149 " pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 121.97 126.47 -4.50 1.80e+00 3.09e-01 6.24e+00 angle pdb=" N VAL B 150 " pdb=" CA VAL B 150 " pdb=" C VAL B 150 " ideal model delta sigma weight residual 109.34 113.31 -3.97 2.08e+00 2.31e-01 3.64e+00 angle pdb=" C GLU C 36 " pdb=" N PRO C 37 " pdb=" CA PRO C 37 " ideal model delta sigma weight residual 120.83 119.10 1.73 1.02e+00 9.61e-01 2.86e+00 ... (remaining 13688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5801 17.42 - 34.83: 575 34.83 - 52.25: 87 52.25 - 69.67: 15 69.67 - 87.09: 15 Dihedral angle restraints: 6493 sinusoidal: 2845 harmonic: 3648 Sorted by residual: dihedral pdb=" CG ARG K 38 " pdb=" CD ARG K 38 " pdb=" NE ARG K 38 " pdb=" CZ ARG K 38 " ideal model delta sinusoidal sigma weight residual -180.00 -137.72 -42.28 2 1.50e+01 4.44e-03 9.66e+00 dihedral pdb=" CB MET K 97 " pdb=" CG MET K 97 " pdb=" SD MET K 97 " pdb=" CE MET K 97 " ideal model delta sinusoidal sigma weight residual 60.00 118.39 -58.39 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB GLU B 12 " pdb=" CG GLU B 12 " pdb=" CD GLU B 12 " pdb=" OE1 GLU B 12 " ideal model delta sinusoidal sigma weight residual 0.00 82.97 -82.97 1 3.00e+01 1.11e-03 9.36e+00 ... (remaining 6490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1142 0.030 - 0.061: 309 0.061 - 0.091: 104 0.091 - 0.121: 30 0.121 - 0.152: 3 Chirality restraints: 1588 Sorted by residual: chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CB VAL A 150 " pdb=" CA VAL A 150 " pdb=" CG1 VAL A 150 " pdb=" CG2 VAL A 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1585 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 33 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO I 34 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 34 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 34 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 145 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO H 146 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.51e-01 pdb=" N PRO H 34 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.012 5.00e-02 4.00e+02 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2403 2.79 - 3.32: 10330 3.32 - 3.85: 15840 3.85 - 4.37: 18075 4.37 - 4.90: 30131 Nonbonded interactions: 76779 Sorted by model distance: nonbonded pdb=" O ARG A 162 " pdb=" NE2 GLN A 166 " model vdw 2.268 3.120 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP A 28 " pdb=" NH2 ARG A 102 " model vdw 2.282 3.120 nonbonded pdb=" O TYR A 106 " pdb=" OG SER A 109 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASP B 28 " pdb=" NH2 ARG B 102 " model vdw 2.303 3.120 ... (remaining 76774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'H' and (resid 2 through 121 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 29 or resid 33 through 175)) selection = (chain 'J' and (resid 2 through 29 or resid 33 through 121 or resid 128 through \ 175)) selection = (chain 'K' and (resid 2 through 29 or resid 33 through 121 or resid 128 through \ 175)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10224 Z= 0.128 Angle : 0.426 4.627 13693 Z= 0.229 Chirality : 0.033 0.152 1588 Planarity : 0.002 0.044 1742 Dihedral : 13.999 87.086 4101 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 aren not related in a simple way. whole: 2.28 (0.26), residues: 1212 helix: 2.22 (0.18), residues: 937 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 45 TYR 0.011 0.001 TYR A 101 PHE 0.013 0.001 PHE B 143 HIS 0.003 0.001 HIS K 160 Details of bonding type rmsd covalent geometry : bond 0.00264 (10224) covalent geometry : angle 0.42625 (13693) hydrogen bonds : bond 0.14939 ( 579) hydrogen bonds : angle 5.05812 ( 1737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9517 (mm-40) cc_final: 0.9272 (mm-40) REVERT: A 17 GLU cc_start: 0.9282 (tt0) cc_final: 0.8963 (tm-30) REVERT: A 46 GLN cc_start: 0.9481 (mt0) cc_final: 0.9084 (tm-30) REVERT: A 97 GLN cc_start: 0.8875 (mt0) cc_final: 0.8444 (mp-120) REVERT: A 104 MET cc_start: 0.9255 (tmm) cc_final: 0.8916 (tmm) REVERT: A 160 LEU cc_start: 0.9588 (tp) cc_final: 0.9373 (tt) REVERT: B 1 MET cc_start: 0.7514 (ptp) cc_final: 0.7103 (ptm) REVERT: B 32 GLN cc_start: 0.9205 (mm110) cc_final: 0.8898 (mm110) REVERT: B 36 GLU cc_start: 0.8929 (tt0) cc_final: 0.8627 (mt-10) REVERT: B 49 GLN cc_start: 0.9487 (mt0) cc_final: 0.8772 (mt0) REVERT: B 143 PHE cc_start: 0.9410 (m-10) cc_final: 0.9031 (m-10) REVERT: B 152 LEU cc_start: 0.9560 (tp) cc_final: 0.9157 (mp) REVERT: C 42 LEU cc_start: 0.9285 (mt) cc_final: 0.9043 (mm) REVERT: C 43 MET cc_start: 0.9219 (mmm) cc_final: 0.8473 (mmm) REVERT: C 45 PHE cc_start: 0.9604 (m-10) cc_final: 0.9127 (m-80) REVERT: C 46 GLN cc_start: 0.9408 (mt0) cc_final: 0.9158 (mt0) REVERT: C 49 GLN cc_start: 0.9417 (mt0) cc_final: 0.9207 (mm110) REVERT: C 112 VAL cc_start: 0.8155 (t) cc_final: 0.7708 (t) REVERT: C 148 LYS cc_start: 0.9596 (mttt) cc_final: 0.9378 (mmmt) REVERT: H 20 MET cc_start: 0.9628 (ttm) cc_final: 0.9268 (tpp) REVERT: H 60 TYR cc_start: 0.9323 (t80) cc_final: 0.9044 (t80) REVERT: H 131 PHE cc_start: 0.9375 (t80) cc_final: 0.8887 (t80) REVERT: I 1 MET cc_start: 0.8572 (ttm) cc_final: 0.8351 (ttp) REVERT: I 16 ASP cc_start: 0.9395 (t70) cc_final: 0.9147 (p0) REVERT: I 17 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8945 (mt-10) REVERT: I 97 MET cc_start: 0.9651 (mmp) cc_final: 0.9435 (mmm) REVERT: I 116 MET cc_start: 0.9422 (mmm) cc_final: 0.9106 (mmm) REVERT: I 169 GLN cc_start: 0.9426 (mt0) cc_final: 0.9218 (mm-40) REVERT: J 17 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8678 (mt-10) REVERT: J 21 LEU cc_start: 0.9789 (tp) cc_final: 0.9569 (pp) REVERT: J 55 LEU cc_start: 0.9783 (tp) cc_final: 0.9562 (pp) REVERT: J 102 GLU cc_start: 0.8935 (tp30) cc_final: 0.8731 (tm-30) REVERT: J 116 MET cc_start: 0.9401 (mmt) cc_final: 0.8981 (mmm) REVERT: K 6 ILE cc_start: 0.9703 (mt) cc_final: 0.9475 (mt) REVERT: K 20 MET cc_start: 0.9504 (ttt) cc_final: 0.9033 (tpp) REVERT: K 25 CYS cc_start: 0.9532 (m) cc_final: 0.9254 (m) REVERT: K 82 HIS cc_start: 0.8874 (t70) cc_final: 0.8440 (t70) REVERT: K 93 TYR cc_start: 0.8554 (t80) cc_final: 0.7872 (t80) REVERT: K 142 ASN cc_start: 0.9152 (t0) cc_final: 0.8947 (m-40) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1011 time to fit residues: 38.4714 Evaluate side-chains 158 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 GLN C 125 GLN H 82 HIS H 88 HIS J 8 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040077 restraints weight = 68610.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041182 restraints weight = 44357.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041936 restraints weight = 33431.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042451 restraints weight = 27575.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042798 restraints weight = 24240.908| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10224 Z= 0.237 Angle : 0.680 9.968 13693 Z= 0.348 Chirality : 0.039 0.136 1588 Planarity : 0.004 0.041 1742 Dihedral : 3.835 15.959 1348 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.82 % Allowed : 10.15 % Favored : 88.03 % 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 aren not related in a simple way. whole: 1.50 (0.25), residues: 1212 helix: 1.52 (0.18), residues: 961 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 85 TYR 0.025 0.002 TYR K 93 PHE 0.022 0.002 PHE B 181 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00510 (10224) covalent geometry : angle 0.68026 (13693) hydrogen bonds : bond 0.04031 ( 579) hydrogen bonds : angle 4.78356 ( 1737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.445 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: A 17 GLU cc_start: 0.9274 (tt0) cc_final: 0.9000 (tm-30) REVERT: A 46 GLN cc_start: 0.9477 (mt0) cc_final: 0.9085 (tm-30) REVERT: B 46 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8258 (tm-30) REVERT: B 49 GLN cc_start: 0.9288 (mt0) cc_final: 0.8921 (mp10) REVERT: B 152 LEU cc_start: 0.9550 (tp) cc_final: 0.9199 (mt) REVERT: C 43 MET cc_start: 0.9212 (mmm) cc_final: 0.8974 (mmm) REVERT: H 20 MET cc_start: 0.9592 (ttm) cc_final: 0.9299 (tpp) REVERT: H 60 TYR cc_start: 0.9287 (t80) cc_final: 0.8965 (t80) REVERT: I 17 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8889 (mt-10) REVERT: J 17 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8588 (mt-10) REVERT: J 25 CYS cc_start: 0.9590 (m) cc_final: 0.9279 (p) REVERT: J 116 MET cc_start: 0.9431 (mmt) cc_final: 0.8909 (mmm) REVERT: K 20 MET cc_start: 0.9442 (ttt) cc_final: 0.8869 (tpp) REVERT: K 82 HIS cc_start: 0.8771 (t70) cc_final: 0.8411 (t70) REVERT: K 86 ASN cc_start: 0.7257 (m110) cc_final: 0.7050 (m110) REVERT: K 131 PHE cc_start: 0.9097 (t80) cc_final: 0.8640 (t80) outliers start: 21 outliers final: 8 residues processed: 181 average time/residue: 0.0828 time to fit residues: 22.0541 Evaluate side-chains 142 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 111 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 125 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.055765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041241 restraints weight = 67961.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042443 restraints weight = 43401.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043220 restraints weight = 32302.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043763 restraints weight = 26592.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044117 restraints weight = 23366.687| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10224 Z= 0.117 Angle : 0.595 9.167 13693 Z= 0.301 Chirality : 0.037 0.179 1588 Planarity : 0.003 0.036 1742 Dihedral : 3.714 15.767 1348 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.47 % Allowed : 13.44 % Favored : 85.08 % 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 aren not related in a simple way. whole: 1.48 (0.25), residues: 1212 helix: 1.48 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 85 TYR 0.014 0.001 TYR C 101 PHE 0.028 0.002 PHE C 181 HIS 0.001 0.000 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00262 (10224) covalent geometry : angle 0.59493 (13693) hydrogen bonds : bond 0.03335 ( 579) hydrogen bonds : angle 4.38247 ( 1737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.493 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: A 17 GLU cc_start: 0.9318 (tt0) cc_final: 0.9012 (tm-30) REVERT: A 35 GLN cc_start: 0.9048 (tt0) cc_final: 0.8617 (tm-30) REVERT: A 46 GLN cc_start: 0.9529 (mt0) cc_final: 0.9156 (tm-30) REVERT: A 104 MET cc_start: 0.9447 (ppp) cc_final: 0.9182 (ppp) REVERT: B 46 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8241 (tm-30) REVERT: B 49 GLN cc_start: 0.9248 (mt0) cc_final: 0.8912 (mt0) REVERT: B 86 MET cc_start: 0.8799 (tpp) cc_final: 0.8570 (tpp) REVERT: B 104 MET cc_start: 0.8720 (ptm) cc_final: 0.8498 (ptm) REVERT: B 120 PHE cc_start: 0.9753 (OUTLIER) cc_final: 0.9552 (t80) REVERT: C 43 MET cc_start: 0.9259 (mmm) cc_final: 0.9007 (mmm) REVERT: C 45 PHE cc_start: 0.9540 (m-10) cc_final: 0.9296 (m-80) REVERT: H 20 MET cc_start: 0.9604 (ttm) cc_final: 0.9313 (tpp) REVERT: I 17 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8863 (mt-10) REVERT: I 30 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7510 (mm) REVERT: J 1 MET cc_start: 0.8520 (pmm) cc_final: 0.8281 (pmm) REVERT: J 17 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8537 (mt-10) REVERT: J 25 CYS cc_start: 0.9574 (m) cc_final: 0.9192 (p) REVERT: J 97 MET cc_start: 0.9503 (mmm) cc_final: 0.9249 (mmm) REVERT: J 116 MET cc_start: 0.9444 (mmt) cc_final: 0.9006 (mmm) REVERT: K 20 MET cc_start: 0.9391 (ttt) cc_final: 0.8875 (tpp) REVERT: K 82 HIS cc_start: 0.8735 (t70) cc_final: 0.8302 (t70) REVERT: K 131 PHE cc_start: 0.9062 (t80) cc_final: 0.8788 (t80) outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 0.0911 time to fit residues: 23.1486 Evaluate side-chains 147 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN J 82 HIS ** K 8 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 = 0.3386 r_free = 0.3386 target = 0.055593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041208 restraints weight = 68622.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042386 restraints weight = 43365.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.043153 restraints weight = 32348.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043696 restraints weight = 26606.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044055 restraints weight = 23376.448| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10224 Z= 0.117 Angle : 0.592 12.064 13693 Z= 0.296 Chirality : 0.038 0.290 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.684 16.224 1348 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.91 % Allowed : 13.79 % Favored : 84.30 % 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 aren not related in a simple way. whole: 1.49 (0.25), residues: 1212 helix: 1.48 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.026 0.001 TYR B 101 PHE 0.046 0.002 PHE C 181 HIS 0.002 0.000 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00264 (10224) covalent geometry : angle 0.59182 (13693) hydrogen bonds : bond 0.02987 ( 579) hydrogen bonds : angle 4.30442 ( 1737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.447 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: A 17 GLU cc_start: 0.9233 (tt0) cc_final: 0.8986 (tm-30) REVERT: A 35 GLN cc_start: 0.9055 (tt0) cc_final: 0.8632 (tm-30) REVERT: A 46 GLN cc_start: 0.9490 (mt0) cc_final: 0.9154 (tm-30) REVERT: B 46 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8222 (tm-30) REVERT: B 49 GLN cc_start: 0.9197 (mt0) cc_final: 0.8913 (mt0) REVERT: B 86 MET cc_start: 0.8720 (tpp) cc_final: 0.8462 (tpp) REVERT: C 43 MET cc_start: 0.9181 (mmm) cc_final: 0.8968 (mmm) REVERT: C 45 PHE cc_start: 0.9529 (m-10) cc_final: 0.9221 (m-80) REVERT: C 107 GLN cc_start: 0.9654 (mt0) cc_final: 0.9199 (mt0) REVERT: C 145 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8584 (mt-10) REVERT: H 20 MET cc_start: 0.9581 (ttm) cc_final: 0.9333 (tpp) REVERT: H 36 ASN cc_start: 0.7100 (t0) cc_final: 0.6840 (t0) REVERT: I 17 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8967 (mt-10) REVERT: I 30 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7478 (mm) REVERT: I 97 MET cc_start: 0.9627 (mmm) cc_final: 0.9383 (mmm) REVERT: J 17 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8458 (mt-10) REVERT: J 25 CYS cc_start: 0.9506 (m) cc_final: 0.9137 (p) REVERT: J 116 MET cc_start: 0.9379 (mmt) cc_final: 0.8857 (mmm) REVERT: K 20 MET cc_start: 0.9381 (ttt) cc_final: 0.8884 (tpp) REVERT: K 21 LEU cc_start: 0.9749 (tp) cc_final: 0.9504 (pp) REVERT: K 82 HIS cc_start: 0.8619 (t70) cc_final: 0.8264 (t70) outliers start: 22 outliers final: 11 residues processed: 165 average time/residue: 0.0874 time to fit residues: 21.4245 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.056152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041821 restraints weight = 67312.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043020 restraints weight = 42473.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043835 restraints weight = 31553.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044380 restraints weight = 25847.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044747 restraints weight = 22615.613| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10224 Z= 0.103 Angle : 0.591 11.825 13693 Z= 0.290 Chirality : 0.037 0.209 1588 Planarity : 0.003 0.032 1742 Dihedral : 3.667 15.629 1348 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.73 % Allowed : 14.57 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.25), residues: 1212 helix: 1.53 (0.18), residues: 948 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 122 TYR 0.011 0.001 TYR B 101 PHE 0.041 0.002 PHE C 181 HIS 0.001 0.000 HIS I 7 Details of bonding type rmsd covalent geometry : bond 0.00232 (10224) covalent geometry : angle 0.59097 (13693) hydrogen bonds : bond 0.02795 ( 579) hydrogen bonds : angle 4.14104 ( 1737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.427 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: A 17 GLU cc_start: 0.9281 (tt0) cc_final: 0.9006 (tm-30) REVERT: A 35 GLN cc_start: 0.9022 (tt0) cc_final: 0.8632 (tm-30) REVERT: A 46 GLN cc_start: 0.9536 (mt0) cc_final: 0.9153 (tm-30) REVERT: B 46 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8282 (tm-30) REVERT: B 49 GLN cc_start: 0.9203 (mt0) cc_final: 0.8916 (mt0) REVERT: B 86 MET cc_start: 0.8826 (tpp) cc_final: 0.8523 (tpp) REVERT: B 104 MET cc_start: 0.8976 (ptm) cc_final: 0.8717 (ptm) REVERT: C 43 MET cc_start: 0.9330 (mmm) cc_final: 0.9069 (mmm) REVERT: C 45 PHE cc_start: 0.9601 (m-10) cc_final: 0.9263 (m-80) REVERT: C 107 GLN cc_start: 0.9680 (mt0) cc_final: 0.9253 (mt0) REVERT: H 20 MET cc_start: 0.9602 (ttm) cc_final: 0.9333 (tpp) REVERT: H 120 MET cc_start: 0.8406 (mmm) cc_final: 0.8115 (mmm) REVERT: I 17 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8938 (mt-10) REVERT: I 30 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7498 (mm) REVERT: I 97 MET cc_start: 0.9667 (mmm) cc_final: 0.9382 (mmm) REVERT: J 17 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8474 (mt-10) REVERT: J 25 CYS cc_start: 0.9575 (m) cc_final: 0.9152 (p) REVERT: J 116 MET cc_start: 0.9469 (mmt) cc_final: 0.8877 (mmm) REVERT: K 20 MET cc_start: 0.9413 (ttt) cc_final: 0.8940 (tpp) REVERT: K 21 LEU cc_start: 0.9738 (tp) cc_final: 0.9490 (pp) REVERT: K 82 HIS cc_start: 0.8603 (t70) cc_final: 0.8257 (t70) outliers start: 20 outliers final: 11 residues processed: 162 average time/residue: 0.0863 time to fit residues: 21.1013 Evaluate side-chains 152 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041838 restraints weight = 65951.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043073 restraints weight = 41840.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.043865 restraints weight = 30749.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044440 restraints weight = 24985.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044825 restraints weight = 21717.083| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10224 Z= 0.103 Angle : 0.609 12.161 13693 Z= 0.294 Chirality : 0.038 0.371 1588 Planarity : 0.003 0.031 1742 Dihedral : 3.678 15.624 1348 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.89 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 16.05 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1212 helix: 1.58 (0.18), residues: 945 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 161 TYR 0.020 0.001 TYR B 106 PHE 0.043 0.002 PHE C 181 HIS 0.001 0.000 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00230 (10224) covalent geometry : angle 0.60889 (13693) hydrogen bonds : bond 0.02742 ( 579) hydrogen bonds : angle 4.07619 ( 1737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.448 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: A 17 GLU cc_start: 0.9214 (tt0) cc_final: 0.8978 (tm-30) REVERT: A 35 GLN cc_start: 0.9113 (tt0) cc_final: 0.8552 (tm-30) REVERT: A 46 GLN cc_start: 0.9509 (mt0) cc_final: 0.9121 (tm-30) REVERT: B 46 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8275 (tm-30) REVERT: B 49 GLN cc_start: 0.9154 (mt0) cc_final: 0.8947 (mt0) REVERT: B 86 MET cc_start: 0.8738 (tpp) cc_final: 0.8442 (tpp) REVERT: C 1 MET cc_start: 0.7648 (ptp) cc_final: 0.7324 (ptp) REVERT: C 43 MET cc_start: 0.9269 (mmm) cc_final: 0.8570 (mmm) REVERT: C 45 PHE cc_start: 0.9567 (m-10) cc_final: 0.9195 (m-80) REVERT: C 46 GLN cc_start: 0.9455 (mt0) cc_final: 0.9070 (mt0) REVERT: H 20 MET cc_start: 0.9571 (ttm) cc_final: 0.9312 (tpp) REVERT: H 120 MET cc_start: 0.8382 (mmm) cc_final: 0.8043 (mmm) REVERT: I 17 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8965 (mt-10) REVERT: I 30 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7506 (mm) REVERT: I 97 MET cc_start: 0.9636 (mmm) cc_final: 0.9381 (mmm) REVERT: I 120 MET cc_start: 0.8591 (pmm) cc_final: 0.8342 (pmm) REVERT: J 17 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8470 (mt-10) REVERT: J 25 CYS cc_start: 0.9515 (m) cc_final: 0.9125 (p) REVERT: J 116 MET cc_start: 0.9385 (mmt) cc_final: 0.8747 (mmm) REVERT: K 20 MET cc_start: 0.9391 (ttt) cc_final: 0.8866 (tpp) REVERT: K 82 HIS cc_start: 0.8577 (t70) cc_final: 0.8208 (t70) REVERT: K 152 LEU cc_start: 0.9687 (mp) cc_final: 0.9432 (tt) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.0864 time to fit residues: 20.7007 Evaluate side-chains 153 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.056237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041792 restraints weight = 67550.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043056 restraints weight = 41687.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043888 restraints weight = 30474.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044449 restraints weight = 24803.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044775 restraints weight = 21569.942| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10224 Z= 0.110 Angle : 0.624 12.056 13693 Z= 0.304 Chirality : 0.038 0.313 1588 Planarity : 0.003 0.030 1742 Dihedral : 3.688 19.232 1348 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 1.99 % Allowed : 16.91 % Favored : 81.09 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1212 helix: 1.60 (0.18), residues: 945 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 161 TYR 0.017 0.001 TYR A 106 PHE 0.046 0.002 PHE C 181 HIS 0.001 0.000 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00248 (10224) covalent geometry : angle 0.62450 (13693) hydrogen bonds : bond 0.02772 ( 579) hydrogen bonds : angle 4.10042 ( 1737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.479 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: A 17 GLU cc_start: 0.9230 (tt0) cc_final: 0.9000 (tm-30) REVERT: A 35 GLN cc_start: 0.9095 (tt0) cc_final: 0.8536 (tm-30) REVERT: A 46 GLN cc_start: 0.9521 (mt0) cc_final: 0.9156 (tm-30) REVERT: A 110 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8917 (mt-10) REVERT: B 46 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8290 (tm-30) REVERT: B 49 GLN cc_start: 0.9175 (mt0) cc_final: 0.8962 (mt0) REVERT: B 86 MET cc_start: 0.8791 (tpp) cc_final: 0.8486 (tpp) REVERT: B 105 LEU cc_start: 0.9118 (mt) cc_final: 0.8747 (mt) REVERT: B 137 MET cc_start: 0.7416 (ptp) cc_final: 0.7195 (ptp) REVERT: C 1 MET cc_start: 0.7612 (ptp) cc_final: 0.7321 (ptp) REVERT: C 43 MET cc_start: 0.9287 (mmm) cc_final: 0.9057 (mmm) REVERT: C 45 PHE cc_start: 0.9558 (m-10) cc_final: 0.9204 (m-80) REVERT: C 137 MET cc_start: 0.8561 (ptp) cc_final: 0.8142 (pmm) REVERT: H 20 MET cc_start: 0.9590 (ttm) cc_final: 0.9320 (tpp) REVERT: H 120 MET cc_start: 0.8483 (mmm) cc_final: 0.8144 (mmm) REVERT: I 1 MET cc_start: 0.8401 (ttp) cc_final: 0.7796 (ttp) REVERT: I 17 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8974 (mt-10) REVERT: I 30 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7541 (mm) REVERT: I 97 MET cc_start: 0.9622 (mmm) cc_final: 0.9386 (mmm) REVERT: J 17 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8504 (mt-10) REVERT: J 25 CYS cc_start: 0.9521 (m) cc_final: 0.9138 (p) REVERT: K 20 MET cc_start: 0.9343 (ttt) cc_final: 0.8869 (tpp) REVERT: K 82 HIS cc_start: 0.8575 (t70) cc_final: 0.8216 (t70) outliers start: 23 outliers final: 14 residues processed: 157 average time/residue: 0.0847 time to fit residues: 20.3597 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041459 restraints weight = 66761.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042650 restraints weight = 43224.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043445 restraints weight = 32153.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043973 restraints weight = 26344.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044339 restraints weight = 23015.536| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10224 Z= 0.128 Angle : 0.635 11.803 13693 Z= 0.312 Chirality : 0.039 0.288 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.726 18.378 1348 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.73 % Allowed : 17.78 % Favored : 80.49 % 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 aren not related in a simple way. whole: 1.58 (0.26), residues: 1212 helix: 1.61 (0.18), residues: 944 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 161 TYR 0.016 0.001 TYR A 106 PHE 0.046 0.002 PHE C 181 HIS 0.002 0.001 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00288 (10224) covalent geometry : angle 0.63474 (13693) hydrogen bonds : bond 0.02940 ( 579) hydrogen bonds : angle 4.23118 ( 1737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.465 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: A 1 MET cc_start: 0.6497 (mtm) cc_final: 0.6262 (mtm) REVERT: A 35 GLN cc_start: 0.9094 (tt0) cc_final: 0.8560 (tm-30) REVERT: A 46 GLN cc_start: 0.9516 (mt0) cc_final: 0.9155 (tm-30) REVERT: B 46 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8261 (tm-30) REVERT: B 49 GLN cc_start: 0.9207 (mt0) cc_final: 0.8962 (mt0) REVERT: B 86 MET cc_start: 0.8739 (tpp) cc_final: 0.8447 (tpp) REVERT: B 105 LEU cc_start: 0.9190 (mt) cc_final: 0.8827 (mt) REVERT: B 137 MET cc_start: 0.7439 (ptp) cc_final: 0.7125 (ptp) REVERT: C 1 MET cc_start: 0.7641 (ptp) cc_final: 0.7340 (ptp) REVERT: C 43 MET cc_start: 0.9289 (mmm) cc_final: 0.9045 (mmm) REVERT: C 45 PHE cc_start: 0.9559 (m-10) cc_final: 0.9174 (m-80) REVERT: C 137 MET cc_start: 0.8487 (ptp) cc_final: 0.8036 (pmm) REVERT: H 20 MET cc_start: 0.9570 (ttm) cc_final: 0.9300 (tpp) REVERT: H 120 MET cc_start: 0.8497 (mmm) cc_final: 0.8149 (mmm) REVERT: I 1 MET cc_start: 0.8454 (ttp) cc_final: 0.7857 (ttp) REVERT: I 17 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9005 (mt-10) REVERT: I 30 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7586 (mm) REVERT: I 68 LEU cc_start: 0.9301 (tt) cc_final: 0.8979 (pp) REVERT: I 97 MET cc_start: 0.9617 (mmm) cc_final: 0.9376 (mmm) REVERT: J 17 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8506 (mt-10) REVERT: J 25 CYS cc_start: 0.9535 (m) cc_final: 0.9178 (p) REVERT: K 20 MET cc_start: 0.9342 (ttt) cc_final: 0.8886 (tpp) REVERT: K 82 HIS cc_start: 0.8542 (t70) cc_final: 0.8230 (t-90) outliers start: 20 outliers final: 16 residues processed: 151 average time/residue: 0.0902 time to fit residues: 20.4131 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.055242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041091 restraints weight = 66848.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042248 restraints weight = 43270.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043012 restraints weight = 32402.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043548 restraints weight = 26641.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.043910 restraints weight = 23230.538| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10224 Z= 0.145 Angle : 0.652 11.465 13693 Z= 0.321 Chirality : 0.039 0.282 1588 Planarity : 0.003 0.037 1742 Dihedral : 3.847 22.272 1348 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 1.65 % Allowed : 18.13 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1212 helix: 1.62 (0.18), residues: 938 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 161 TYR 0.017 0.001 TYR A 106 PHE 0.047 0.002 PHE C 181 HIS 0.002 0.001 HIS J 7 Details of bonding type rmsd covalent geometry : bond 0.00324 (10224) covalent geometry : angle 0.65150 (13693) hydrogen bonds : bond 0.03057 ( 579) hydrogen bonds : angle 4.31358 ( 1737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.520 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: A 35 GLN cc_start: 0.9094 (tt0) cc_final: 0.8560 (tm-30) REVERT: A 46 GLN cc_start: 0.9511 (mt0) cc_final: 0.9164 (tm-30) REVERT: B 46 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8252 (tm-30) REVERT: B 49 GLN cc_start: 0.9201 (mt0) cc_final: 0.8933 (mt0) REVERT: B 86 MET cc_start: 0.8743 (tpp) cc_final: 0.8447 (tpp) REVERT: B 104 MET cc_start: 0.8506 (ptm) cc_final: 0.8293 (ptm) REVERT: C 43 MET cc_start: 0.9254 (mmm) cc_final: 0.8560 (mmm) REVERT: C 45 PHE cc_start: 0.9540 (m-10) cc_final: 0.9164 (m-80) REVERT: C 46 GLN cc_start: 0.9432 (mt0) cc_final: 0.9059 (mt0) REVERT: C 86 MET cc_start: 0.9755 (tpp) cc_final: 0.9409 (tmm) REVERT: C 137 MET cc_start: 0.8538 (ptp) cc_final: 0.8078 (pmm) REVERT: H 20 MET cc_start: 0.9575 (ttm) cc_final: 0.9313 (tpp) REVERT: H 120 MET cc_start: 0.8539 (mmm) cc_final: 0.8175 (mmm) REVERT: I 1 MET cc_start: 0.8469 (ttp) cc_final: 0.7899 (ttp) REVERT: I 17 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9027 (mt-10) REVERT: I 30 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7606 (mm) REVERT: I 68 LEU cc_start: 0.9330 (tt) cc_final: 0.9013 (pp) REVERT: I 97 MET cc_start: 0.9625 (mmm) cc_final: 0.9393 (mmm) REVERT: J 17 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8551 (mt-10) REVERT: J 25 CYS cc_start: 0.9542 (m) cc_final: 0.9198 (p) REVERT: K 20 MET cc_start: 0.9390 (ttt) cc_final: 0.8923 (tpp) REVERT: K 82 HIS cc_start: 0.8526 (t70) cc_final: 0.8224 (t-90) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.0987 time to fit residues: 21.6664 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.055960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041786 restraints weight = 65005.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043027 restraints weight = 41605.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.043846 restraints weight = 30585.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044379 restraints weight = 24869.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044761 restraints weight = 21622.750| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10224 Z= 0.110 Angle : 0.663 12.660 13693 Z= 0.318 Chirality : 0.038 0.281 1588 Planarity : 0.003 0.038 1742 Dihedral : 3.779 23.536 1348 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.05 % Favored : 96.78 % Rotamer: Outliers : 1.30 % Allowed : 18.91 % Favored : 79.79 % 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 aren not related in a simple way. whole: 1.56 (0.26), residues: 1212 helix: 1.62 (0.18), residues: 939 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.014 0.001 TYR A 106 PHE 0.048 0.002 PHE C 181 HIS 0.001 0.000 HIS K 82 Details of bonding type rmsd covalent geometry : bond 0.00247 (10224) covalent geometry : angle 0.66311 (13693) hydrogen bonds : bond 0.02847 ( 579) hydrogen bonds : angle 4.15600 ( 1737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.471 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: A 35 GLN cc_start: 0.9088 (tt0) cc_final: 0.8535 (tm-30) REVERT: A 46 GLN cc_start: 0.9516 (mt0) cc_final: 0.9170 (tm-30) REVERT: B 46 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8234 (tm-30) REVERT: B 49 GLN cc_start: 0.9161 (mt0) cc_final: 0.8943 (mt0) REVERT: B 86 MET cc_start: 0.8752 (tpp) cc_final: 0.8445 (tpp) REVERT: B 137 MET cc_start: 0.7221 (ptp) cc_final: 0.7006 (ptp) REVERT: C 45 PHE cc_start: 0.9554 (m-10) cc_final: 0.9129 (m-80) REVERT: C 86 MET cc_start: 0.9750 (tpp) cc_final: 0.9407 (tmm) REVERT: C 137 MET cc_start: 0.8446 (ptp) cc_final: 0.8060 (pmm) REVERT: H 20 MET cc_start: 0.9563 (ttm) cc_final: 0.9303 (tpp) REVERT: H 104 LEU cc_start: 0.9102 (mt) cc_final: 0.8729 (mp) REVERT: H 120 MET cc_start: 0.8527 (mmm) cc_final: 0.8194 (mmm) REVERT: I 1 MET cc_start: 0.8565 (ttp) cc_final: 0.8011 (ttp) REVERT: I 17 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9058 (mp0) REVERT: I 30 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7648 (mm) REVERT: I 68 LEU cc_start: 0.9269 (tt) cc_final: 0.8966 (pp) REVERT: I 97 MET cc_start: 0.9600 (mmm) cc_final: 0.9376 (mmm) REVERT: J 17 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8524 (mt-10) REVERT: J 25 CYS cc_start: 0.9532 (m) cc_final: 0.9182 (p) REVERT: J 116 MET cc_start: 0.9319 (tpp) cc_final: 0.9059 (mmm) REVERT: K 20 MET cc_start: 0.9374 (ttt) cc_final: 0.8918 (tpp) REVERT: K 82 HIS cc_start: 0.8495 (t70) cc_final: 0.8177 (t-90) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.0904 time to fit residues: 20.9981 Evaluate side-chains 148 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.056514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042311 restraints weight = 65528.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043520 restraints weight = 41926.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044381 restraints weight = 30987.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044945 restraints weight = 25112.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045327 restraints weight = 21707.370| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10224 Z= 0.112 Angle : 0.714 16.236 13693 Z= 0.334 Chirality : 0.039 0.389 1588 Planarity : 0.003 0.043 1742 Dihedral : 3.747 24.482 1348 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.30 % Allowed : 19.08 % Favored : 79.62 % 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 aren not related in a simple way. whole: 1.53 (0.26), residues: 1212 helix: 1.60 (0.18), residues: 939 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.016 0.001 TYR A 8 PHE 0.049 0.002 PHE C 181 HIS 0.001 0.000 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00249 (10224) covalent geometry : angle 0.71424 (13693) hydrogen bonds : bond 0.02781 ( 579) hydrogen bonds : angle 4.13944 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.70 seconds wall clock time: 31 minutes 45.16 seconds (1905.16 seconds total)