Starting phenix.real_space_refine on Thu Jul 31 16:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynn_39428/07_2025/8ynn_39428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynn_39428/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ynn_39428/07_2025/8ynn_39428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynn_39428/07_2025/8ynn_39428.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynn_39428/07_2025/8ynn_39428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynn_39428/07_2025/8ynn_39428.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.05, per 1000 atoms: 0.70 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.49 Time building geometry restraints manager: 2.95 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS K 160 PHE 0.013 0.001 PHE B 143 TYR 0.011 0.001 TYR A 101 ARG 0.003 0.000 ARG I 45 Details of bonding type rmsd hydrogen bonds : bond 0.14939 ( 579) hydrogen bonds : angle 5.05812 ( 1737) covalent geometry : bond 0.00264 (10224) covalent geometry : angle 0.42625 (13693) *********************** 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 : 1.217 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: 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: 0.8962 (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: 0.8938 (tmm) REVERT: A 160 LEU cc_start: 0.9588 (tp) cc_final: 0.9372 (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: 0.9156 (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: 0.8474 (mmm) REVERT: C 45 PHE cc_start: 0.9604 (m-10) cc_final: 0.9133 (m-80) REVERT: C 46 GLN cc_start: 0.9408 (mt0) cc_final: 0.9157 (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: 0.8345 (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: 0.8947 (mt-10) REVERT: I 20 MET cc_start: 0.9564 (ttm) cc_final: 0.9194 (ttm) REVERT: I 97 MET cc_start: 0.9651 (mmp) cc_final: 0.9437 (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: 0.9038 (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: 0.8441 (t70) REVERT: K 93 TYR cc_start: 0.8554 (t80) cc_final: 0.7807 (t80) REVERT: K 142 ASN cc_start: 0.9152 (t0) cc_final: 0.8946 (m-40) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2122 time to fit residues: 80.0680 Evaluate side-chains 157 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 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 = 0.3381 r_free = 0.3381 target = 0.055755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.042097 restraints weight = 66159.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042867 restraints weight = 40058.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043257 restraints weight = 30104.652| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2444 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= 0.153 Angle : 0.601 10.734 13693 Z= 0.310 Chirality : 0.037 0.139 1588 Planarity : 0.003 0.040 1742 Dihedral : 3.615 15.505 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.73 % Allowed : 9.02 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1212 helix: 1.64 (0.18), residues: 964 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 82 PHE 0.020 0.002 PHE A 181 TYR 0.022 0.001 TYR K 93 ARG 0.005 0.000 ARG B 114 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 579) hydrogen bonds : angle 4.45306 ( 1737) covalent geometry : bond 0.00336 (10224) covalent geometry : angle 0.60124 (13693) *********************** 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 196 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.298 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: A 17 GLU cc_start: 0.9306 (tt0) cc_final: 0.9010 (tm-30) REVERT: A 46 GLN cc_start: 0.9500 (mt0) cc_final: 0.9111 (tm-30) REVERT: A 104 MET cc_start: 0.9456 (tmm) cc_final: 0.9248 (ppp) REVERT: B 46 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8211 (tm-30) REVERT: B 49 GLN cc_start: 0.9335 (mt0) cc_final: 0.8981 (mt0) REVERT: B 86 MET cc_start: 0.8878 (tpp) cc_final: 0.8648 (tpp) REVERT: B 104 MET cc_start: 0.8866 (ptm) cc_final: 0.8652 (ptm) REVERT: B 152 LEU cc_start: 0.9546 (tp) cc_final: 0.9120 (mt) REVERT: C 43 MET cc_start: 0.9297 (mmm) cc_final: 0.9016 (mmm) REVERT: C 45 PHE cc_start: 0.9602 (m-10) cc_final: 0.9247 (m-80) REVERT: C 107 GLN cc_start: 0.9679 (mt0) cc_final: 0.9289 (mt0) REVERT: H 20 MET cc_start: 0.9618 (ttm) cc_final: 0.9295 (tpp) REVERT: I 16 ASP cc_start: 0.9451 (t70) cc_final: 0.9221 (p0) REVERT: I 17 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8944 (mt-10) REVERT: I 30 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7498 (mm) REVERT: I 97 MET cc_start: 0.9742 (mmp) cc_final: 0.9526 (mmm) REVERT: I 116 MET cc_start: 0.9358 (mmm) cc_final: 0.9040 (mmm) REVERT: J 1 MET cc_start: 0.8597 (pmm) cc_final: 0.8335 (pmm) REVERT: J 17 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8536 (mt-10) REVERT: J 25 CYS cc_start: 0.9644 (m) cc_final: 0.9237 (p) REVERT: J 116 MET cc_start: 0.9481 (mmt) cc_final: 0.9008 (mmm) REVERT: K 20 MET cc_start: 0.9444 (ttt) cc_final: 0.8875 (tpp) REVERT: K 82 HIS cc_start: 0.8739 (t70) cc_final: 0.8371 (t70) REVERT: K 86 ASN cc_start: 0.7236 (m110) cc_final: 0.7025 (m110) REVERT: K 131 PHE cc_start: 0.9055 (t80) cc_final: 0.8544 (t80) outliers start: 20 outliers final: 5 residues processed: 189 average time/residue: 0.1990 time to fit residues: 54.5117 Evaluate side-chains 145 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE 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 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041244 restraints weight = 67472.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042359 restraints weight = 43083.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043175 restraints weight = 32370.175| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10224 Z= 0.126 Angle : 0.604 11.420 13693 Z= 0.301 Chirality : 0.038 0.191 1588 Planarity : 0.003 0.036 1742 Dihedral : 3.656 15.458 1348 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.04 % Allowed : 12.58 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1212 helix: 1.50 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 82 PHE 0.027 0.002 PHE C 181 TYR 0.019 0.001 TYR H 60 ARG 0.003 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 579) hydrogen bonds : angle 4.32596 ( 1737) covalent geometry : bond 0.00288 (10224) covalent geometry : angle 0.60438 (13693) *********************** 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 167 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.202 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: 0.9297 (tt0) cc_final: 0.9021 (tm-30) REVERT: A 35 GLN cc_start: 0.9081 (tt0) cc_final: 0.8627 (tm-30) REVERT: A 46 GLN cc_start: 0.9524 (mt0) cc_final: 0.9140 (tm-30) REVERT: B 46 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8215 (tm-30) REVERT: B 49 GLN cc_start: 0.9278 (mt0) cc_final: 0.8953 (mt0) REVERT: B 86 MET cc_start: 0.8843 (tpp) cc_final: 0.8561 (tpp) REVERT: B 104 MET cc_start: 0.8904 (ptm) cc_final: 0.8588 (ptm) REVERT: C 43 MET cc_start: 0.9329 (mmm) cc_final: 0.9053 (mmm) REVERT: C 45 PHE cc_start: 0.9576 (m-10) cc_final: 0.9253 (m-80) REVERT: H 20 MET cc_start: 0.9607 (ttm) cc_final: 0.9316 (tpp) REVERT: H 36 ASN cc_start: 0.7172 (t0) cc_final: 0.6895 (t0) REVERT: I 16 ASP cc_start: 0.9463 (t70) cc_final: 0.9250 (p0) REVERT: I 17 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8911 (mt-10) REVERT: I 30 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7525 (mm) REVERT: I 97 MET cc_start: 0.9724 (mmp) cc_final: 0.9468 (mmm) REVERT: I 116 MET cc_start: 0.9318 (mmm) cc_final: 0.9079 (mmm) REVERT: J 1 MET cc_start: 0.8476 (pmm) cc_final: 0.8163 (pmm) REVERT: J 17 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8555 (mt-10) REVERT: J 25 CYS cc_start: 0.9583 (m) cc_final: 0.9203 (p) REVERT: J 116 MET cc_start: 0.9451 (mmt) cc_final: 0.8927 (mmm) REVERT: K 20 MET cc_start: 0.9387 (ttt) cc_final: 0.8891 (tpp) REVERT: K 82 HIS cc_start: 0.8752 (t70) cc_final: 0.8335 (t70) REVERT: K 131 PHE cc_start: 0.9140 (t80) cc_final: 0.8911 (t80) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.1936 time to fit residues: 45.9124 Evaluate side-chains 143 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 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 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 111 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 = 0.3358 r_free = 0.3358 target = 0.054895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040454 restraints weight = 68009.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041587 restraints weight = 43900.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042345 restraints weight = 32958.483| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10224 Z= 0.176 Angle : 0.614 10.211 13693 Z= 0.312 Chirality : 0.038 0.247 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.758 16.031 1348 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.25 % Allowed : 12.40 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1212 helix: 1.42 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 82 PHE 0.047 0.002 PHE C 181 TYR 0.026 0.002 TYR B 101 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 579) hydrogen bonds : angle 4.51702 ( 1737) covalent geometry : bond 0.00389 (10224) covalent geometry : angle 0.61414 (13693) *********************** 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 170 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.221 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: 0.9353 (tt0) cc_final: 0.9010 (tm-30) REVERT: A 35 GLN cc_start: 0.9061 (tt0) cc_final: 0.8574 (tm-30) REVERT: A 46 GLN cc_start: 0.9547 (mt0) cc_final: 0.9170 (tm-30) REVERT: B 46 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8256 (tm-30) REVERT: B 49 GLN cc_start: 0.9282 (mt0) cc_final: 0.8949 (mt0) REVERT: B 86 MET cc_start: 0.8917 (tpp) cc_final: 0.8628 (tpp) REVERT: C 43 MET cc_start: 0.9349 (mmm) cc_final: 0.9080 (mmm) REVERT: C 45 PHE cc_start: 0.9570 (m-10) cc_final: 0.9231 (m-80) REVERT: C 145 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8737 (mt-10) REVERT: H 20 MET cc_start: 0.9620 (ttm) cc_final: 0.9365 (tpp) REVERT: I 17 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8921 (mt-10) REVERT: I 30 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7603 (mm) REVERT: I 97 MET cc_start: 0.9710 (mmp) cc_final: 0.9426 (mmm) REVERT: I 116 MET cc_start: 0.9298 (mmm) cc_final: 0.9038 (mmm) REVERT: J 17 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8567 (mt-10) REVERT: J 25 CYS cc_start: 0.9612 (m) cc_final: 0.9270 (p) REVERT: J 116 MET cc_start: 0.9451 (mmt) cc_final: 0.8856 (mmm) REVERT: K 20 MET cc_start: 0.9417 (ttt) cc_final: 0.8901 (tpp) REVERT: K 82 HIS cc_start: 0.8659 (t70) cc_final: 0.8345 (t-90) REVERT: K 131 PHE cc_start: 0.9223 (t80) cc_final: 0.8983 (t80) outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 0.1942 time to fit residues: 46.7855 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 164 LEU Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 ILE 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 66 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.054751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040298 restraints weight = 68168.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041429 restraints weight = 43912.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042184 restraints weight = 32953.190| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10224 Z= 0.169 Angle : 0.616 9.835 13693 Z= 0.310 Chirality : 0.038 0.202 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.861 15.933 1348 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.43 % Allowed : 13.96 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1212 helix: 1.32 (0.18), residues: 965 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 82 PHE 0.043 0.002 PHE C 181 TYR 0.014 0.001 TYR B 101 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 579) hydrogen bonds : angle 4.50200 ( 1737) covalent geometry : bond 0.00374 (10224) covalent geometry : angle 0.61648 (13693) *********************** 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 164 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.252 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: A 35 GLN cc_start: 0.9097 (tt0) cc_final: 0.8618 (tm-30) REVERT: A 46 GLN cc_start: 0.9554 (mt0) cc_final: 0.9170 (tm-30) REVERT: B 46 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8256 (tm-30) REVERT: B 86 MET cc_start: 0.8925 (tpp) cc_final: 0.8642 (tpp) REVERT: C 43 MET cc_start: 0.9376 (mmm) cc_final: 0.8843 (mmm) REVERT: C 46 GLN cc_start: 0.9444 (mt0) cc_final: 0.9058 (mp10) REVERT: H 20 MET cc_start: 0.9624 (ttm) cc_final: 0.9349 (tpp) REVERT: H 120 MET cc_start: 0.8466 (mmm) cc_final: 0.8112 (mmm) REVERT: I 17 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8934 (mt-10) REVERT: I 30 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7634 (mm) REVERT: I 68 LEU cc_start: 0.9489 (tp) cc_final: 0.9257 (tt) REVERT: I 97 MET cc_start: 0.9710 (mmp) cc_final: 0.9412 (mmm) REVERT: I 116 MET cc_start: 0.9289 (mmm) cc_final: 0.9032 (mmm) REVERT: J 17 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8608 (mt-10) REVERT: J 25 CYS cc_start: 0.9612 (m) cc_final: 0.9271 (p) REVERT: K 20 MET cc_start: 0.9432 (ttt) cc_final: 0.8915 (tpp) REVERT: K 82 HIS cc_start: 0.8620 (t70) cc_final: 0.8328 (t-90) REVERT: K 131 PHE cc_start: 0.9249 (t80) cc_final: 0.9002 (t80) outliers start: 28 outliers final: 18 residues processed: 154 average time/residue: 0.1733 time to fit residues: 40.6536 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 66 LEU 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 41 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.055806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041429 restraints weight = 66780.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042542 restraints weight = 42673.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043352 restraints weight = 32060.458| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10224 Z= 0.107 Angle : 0.612 11.606 13693 Z= 0.296 Chirality : 0.038 0.254 1588 Planarity : 0.003 0.031 1742 Dihedral : 3.757 15.393 1348 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 2.08 % Allowed : 15.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1212 helix: 1.52 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 88 PHE 0.043 0.002 PHE C 181 TYR 0.011 0.001 TYR A 101 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 579) hydrogen bonds : angle 4.23562 ( 1737) covalent geometry : bond 0.00242 (10224) covalent geometry : angle 0.61151 (13693) *********************** 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 167 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.358 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: A 35 GLN cc_start: 0.9080 (tt0) cc_final: 0.8611 (tm-30) REVERT: A 46 GLN cc_start: 0.9553 (mt0) cc_final: 0.9159 (tm-30) REVERT: B 46 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8237 (tm-30) REVERT: B 49 GLN cc_start: 0.9240 (mt0) cc_final: 0.8922 (mt0) REVERT: B 86 MET cc_start: 0.8867 (tpp) cc_final: 0.8566 (tpp) REVERT: C 43 MET cc_start: 0.9345 (mmm) cc_final: 0.8635 (mmm) REVERT: C 46 GLN cc_start: 0.9437 (mt0) cc_final: 0.9052 (mt0) REVERT: C 107 GLN cc_start: 0.9673 (mt0) cc_final: 0.9237 (mt0) REVERT: H 20 MET cc_start: 0.9625 (ttm) cc_final: 0.9355 (tpp) REVERT: H 120 MET cc_start: 0.8470 (mmm) cc_final: 0.8097 (mmm) REVERT: I 1 MET cc_start: 0.8292 (ttp) cc_final: 0.7444 (ttp) REVERT: I 17 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8978 (mt-10) REVERT: I 30 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7661 (mm) REVERT: I 97 MET cc_start: 0.9694 (mmp) cc_final: 0.9393 (mmm) REVERT: I 116 MET cc_start: 0.9303 (mmm) cc_final: 0.9037 (mmm) REVERT: J 17 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8541 (mt-10) REVERT: J 25 CYS cc_start: 0.9587 (m) cc_final: 0.9205 (p) REVERT: J 116 MET cc_start: 0.9512 (tpp) cc_final: 0.8944 (mmm) REVERT: K 20 MET cc_start: 0.9414 (ttt) cc_final: 0.8873 (tpp) REVERT: K 82 HIS cc_start: 0.8604 (t70) cc_final: 0.8323 (t-90) REVERT: K 131 PHE cc_start: 0.9226 (t80) cc_final: 0.8987 (t80) outliers start: 24 outliers final: 13 residues processed: 158 average time/residue: 0.1788 time to fit residues: 42.7147 Evaluate side-chains 150 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 146 MET 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 42 LEU 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 100 ILE 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 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.054713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040039 restraints weight = 68773.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041168 restraints weight = 44616.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041914 restraints weight = 33577.546| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10224 Z= 0.176 Angle : 0.641 10.189 13693 Z= 0.319 Chirality : 0.038 0.157 1588 Planarity : 0.003 0.031 1742 Dihedral : 3.926 16.649 1348 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 2.08 % Allowed : 15.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1212 helix: 1.46 (0.18), residues: 944 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 7 PHE 0.042 0.002 PHE C 181 TYR 0.016 0.002 TYR A 8 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 579) hydrogen bonds : angle 4.56235 ( 1737) covalent geometry : bond 0.00388 (10224) covalent geometry : angle 0.64080 (13693) *********************** 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 156 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.240 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 35 GLN cc_start: 0.9113 (tt0) cc_final: 0.8630 (tm-30) REVERT: A 46 GLN cc_start: 0.9564 (mt0) cc_final: 0.9165 (tm-30) REVERT: B 86 MET cc_start: 0.8943 (tpp) cc_final: 0.8646 (tpp) REVERT: C 43 MET cc_start: 0.9359 (mmm) cc_final: 0.8823 (mmm) REVERT: C 46 GLN cc_start: 0.9447 (mt0) cc_final: 0.9038 (mp10) REVERT: C 53 MET cc_start: 0.8794 (mtm) cc_final: 0.8448 (ttp) REVERT: C 86 MET cc_start: 0.9796 (tpp) cc_final: 0.9528 (tmm) REVERT: H 20 MET cc_start: 0.9633 (ttm) cc_final: 0.9370 (tpp) REVERT: H 120 MET cc_start: 0.8589 (mmm) cc_final: 0.8183 (mmm) REVERT: I 1 MET cc_start: 0.8289 (ttp) cc_final: 0.7483 (ttp) REVERT: I 17 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9026 (mt-10) REVERT: I 30 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7735 (mm) REVERT: I 97 MET cc_start: 0.9715 (mmp) cc_final: 0.9367 (mmm) REVERT: J 17 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8604 (mt-10) REVERT: J 25 CYS cc_start: 0.9614 (m) cc_final: 0.9267 (p) REVERT: K 1 MET cc_start: 0.7449 (ptm) cc_final: 0.7223 (ttt) REVERT: K 20 MET cc_start: 0.9384 (ttt) cc_final: 0.8916 (tpp) REVERT: K 82 HIS cc_start: 0.8593 (t70) cc_final: 0.8313 (t-90) REVERT: K 131 PHE cc_start: 0.9322 (t80) cc_final: 0.9039 (t80) REVERT: K 152 LEU cc_start: 0.9715 (mp) cc_final: 0.9462 (tt) outliers start: 24 outliers final: 17 residues processed: 147 average time/residue: 0.1786 time to fit residues: 39.7873 Evaluate side-chains 147 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 162 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 100 ILE 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 11 optimal weight: 10.0000 chunk 77 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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** K 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.055762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041377 restraints weight = 65877.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042564 restraints weight = 42199.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043354 restraints weight = 31244.439| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10224 Z= 0.109 Angle : 0.630 11.984 13693 Z= 0.304 Chirality : 0.037 0.182 1588 Planarity : 0.003 0.030 1742 Dihedral : 3.764 16.632 1348 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.70 % Rotamer: Outliers : 2.08 % Allowed : 16.39 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1212 helix: 1.57 (0.18), residues: 943 sheet: None (None), residues: 0 loop : -0.96 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 88 PHE 0.043 0.002 PHE C 181 TYR 0.013 0.001 TYR K 93 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 579) hydrogen bonds : angle 4.21344 ( 1737) covalent geometry : bond 0.00248 (10224) covalent geometry : angle 0.62988 (13693) *********************** 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 161 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.195 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: A 1 MET cc_start: 0.5722 (ptt) cc_final: 0.5156 (mtm) REVERT: A 35 GLN cc_start: 0.9078 (tt0) cc_final: 0.8593 (tm-30) REVERT: A 46 GLN cc_start: 0.9518 (mt0) cc_final: 0.9145 (tm-30) REVERT: B 46 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8157 (tm-30) REVERT: B 49 GLN cc_start: 0.9174 (mt0) cc_final: 0.8921 (mt0) REVERT: B 86 MET cc_start: 0.8796 (tpp) cc_final: 0.8504 (tpp) REVERT: C 1 MET cc_start: 0.7659 (ptp) cc_final: 0.7366 (ptp) REVERT: C 43 MET cc_start: 0.9274 (mmm) cc_final: 0.8632 (mmm) REVERT: C 46 GLN cc_start: 0.9390 (mt0) cc_final: 0.9121 (mt0) REVERT: C 53 MET cc_start: 0.8700 (mtm) cc_final: 0.8387 (ttp) REVERT: C 107 GLN cc_start: 0.9694 (mt0) cc_final: 0.9204 (mt0) REVERT: H 20 MET cc_start: 0.9586 (ttm) cc_final: 0.9331 (tpp) REVERT: H 120 MET cc_start: 0.8509 (mmm) cc_final: 0.8160 (mmm) REVERT: I 1 MET cc_start: 0.8460 (ttp) cc_final: 0.7624 (ttp) REVERT: I 17 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9017 (mt-10) REVERT: I 30 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7712 (mm) REVERT: I 97 MET cc_start: 0.9640 (mmp) cc_final: 0.9297 (mmm) REVERT: J 17 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8532 (mt-10) REVERT: J 25 CYS cc_start: 0.9527 (m) cc_final: 0.9161 (p) REVERT: J 116 MET cc_start: 0.9355 (tpp) cc_final: 0.8940 (mmm) REVERT: K 20 MET cc_start: 0.9345 (ttt) cc_final: 0.8878 (tpp) REVERT: K 82 HIS cc_start: 0.8563 (t70) cc_final: 0.8277 (t70) outliers start: 24 outliers final: 13 residues processed: 152 average time/residue: 0.1804 time to fit residues: 40.9090 Evaluate side-chains 148 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 162 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 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 91 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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** K 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.056045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041681 restraints weight = 66144.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042891 restraints weight = 42486.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.043688 restraints weight = 31431.713| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4263 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= 0.111 Angle : 0.643 12.340 13693 Z= 0.313 Chirality : 0.038 0.182 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.743 15.571 1348 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 1.39 % Allowed : 17.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1212 helix: 1.50 (0.18), residues: 943 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 7 PHE 0.048 0.002 PHE C 181 TYR 0.016 0.001 TYR B 106 ARG 0.003 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 579) hydrogen bonds : angle 4.23564 ( 1737) covalent geometry : bond 0.00252 (10224) covalent geometry : angle 0.64291 (13693) *********************** 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 159 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.216 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 1 MET cc_start: 0.5696 (ptt) cc_final: 0.5204 (mtm) REVERT: A 35 GLN cc_start: 0.9080 (tt0) cc_final: 0.8595 (tm-30) REVERT: A 46 GLN cc_start: 0.9536 (mt0) cc_final: 0.9159 (tm-30) REVERT: B 46 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8170 (tm-30) REVERT: B 49 GLN cc_start: 0.9167 (mt0) cc_final: 0.8932 (mt0) REVERT: B 86 MET cc_start: 0.8863 (tpp) cc_final: 0.8555 (tpp) REVERT: B 105 LEU cc_start: 0.9152 (mt) cc_final: 0.8787 (mt) REVERT: C 1 MET cc_start: 0.7652 (ptp) cc_final: 0.7378 (ptp) REVERT: C 43 MET cc_start: 0.9313 (mmm) cc_final: 0.8626 (mmm) REVERT: C 46 GLN cc_start: 0.9410 (mt0) cc_final: 0.9073 (mt0) REVERT: C 53 MET cc_start: 0.8721 (mtm) cc_final: 0.8388 (ttp) REVERT: C 107 GLN cc_start: 0.9704 (mt0) cc_final: 0.9217 (mt0) REVERT: C 137 MET cc_start: 0.8477 (ptp) cc_final: 0.7873 (pmm) REVERT: H 20 MET cc_start: 0.9598 (ttm) cc_final: 0.9335 (tpp) REVERT: H 120 MET cc_start: 0.8548 (mmm) cc_final: 0.8193 (mmm) REVERT: I 1 MET cc_start: 0.8484 (ttp) cc_final: 0.7671 (ttp) REVERT: I 17 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9025 (mt-10) REVERT: I 30 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7858 (mm) REVERT: I 97 MET cc_start: 0.9659 (mmp) cc_final: 0.9290 (mmm) REVERT: J 17 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8545 (mt-10) REVERT: J 25 CYS cc_start: 0.9544 (m) cc_final: 0.9156 (p) REVERT: J 116 MET cc_start: 0.9411 (tpp) cc_final: 0.9100 (mmm) REVERT: K 20 MET cc_start: 0.9358 (ttt) cc_final: 0.8926 (tpp) REVERT: K 82 HIS cc_start: 0.8525 (t70) cc_final: 0.8189 (t70) outliers start: 16 outliers final: 14 residues processed: 153 average time/residue: 0.1833 time to fit residues: 41.7452 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 : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 162 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 11 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039186 restraints weight = 69182.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040278 restraints weight = 45006.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041001 restraints weight = 34069.762| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10224 Z= 0.281 Angle : 0.788 11.319 13693 Z= 0.392 Chirality : 0.041 0.210 1588 Planarity : 0.004 0.040 1742 Dihedral : 4.192 18.201 1348 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 1.82 % Allowed : 18.30 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1212 helix: 1.20 (0.18), residues: 939 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 7 PHE 0.048 0.003 PHE C 181 TYR 0.024 0.002 TYR A 8 ARG 0.012 0.001 ARG K 122 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 579) hydrogen bonds : angle 4.93099 ( 1737) covalent geometry : bond 0.00599 (10224) covalent geometry : angle 0.78818 (13693) ********************** 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 147 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.195 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 35 GLN cc_start: 0.9152 (tt0) cc_final: 0.8619 (tm-30) REVERT: A 46 GLN cc_start: 0.9555 (mt0) cc_final: 0.9197 (tm-30) REVERT: B 86 MET cc_start: 0.8940 (tpp) cc_final: 0.8630 (tpp) REVERT: C 43 MET cc_start: 0.9331 (mmm) cc_final: 0.8805 (mmm) REVERT: C 46 GLN cc_start: 0.9460 (mt0) cc_final: 0.9057 (mp10) REVERT: C 53 MET cc_start: 0.8766 (mtm) cc_final: 0.8465 (ttp) REVERT: C 137 MET cc_start: 0.8676 (ptp) cc_final: 0.8411 (pmm) REVERT: H 20 MET cc_start: 0.9630 (ttm) cc_final: 0.9345 (tpp) REVERT: H 120 MET cc_start: 0.8621 (mmm) cc_final: 0.8248 (mmm) REVERT: I 1 MET cc_start: 0.8348 (ttp) cc_final: 0.7562 (ttp) REVERT: I 17 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9038 (mt-10) REVERT: I 30 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7747 (mm) REVERT: I 97 MET cc_start: 0.9683 (mmp) cc_final: 0.9364 (mmm) REVERT: J 17 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8644 (mt-10) REVERT: J 25 CYS cc_start: 0.9621 (m) cc_final: 0.9311 (p) REVERT: K 20 MET cc_start: 0.9399 (ttt) cc_final: 0.8966 (tpp) outliers start: 21 outliers final: 18 residues processed: 139 average time/residue: 0.1742 time to fit residues: 36.9238 Evaluate side-chains 141 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 137 MET 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 162 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 J residue 68 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 133 ASP 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 86 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** 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 = 0.3380 r_free = 0.3380 target = 0.055614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041132 restraints weight = 67843.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042283 restraints weight = 43795.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043071 restraints weight = 32956.192| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4481 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= 0.118 Angle : 0.700 12.747 13693 Z= 0.335 Chirality : 0.040 0.353 1588 Planarity : 0.003 0.044 1742 Dihedral : 3.932 15.489 1348 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.95 % Rotamer: Outliers : 1.73 % Allowed : 18.30 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1212 helix: 1.37 (0.18), residues: 939 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 82 PHE 0.060 0.003 PHE H 131 TYR 0.011 0.001 TYR K 93 ARG 0.004 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 579) hydrogen bonds : angle 4.41981 ( 1737) covalent geometry : bond 0.00265 (10224) covalent geometry : angle 0.69980 (13693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3150.40 seconds wall clock time: 55 minutes 30.66 seconds (3330.66 seconds total)