Starting phenix.real_space_refine on Sun Jan 19 11:06:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ynn_39428/01_2025/8ynn_39428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ynn_39428/01_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_39428/01_2025/8ynn_39428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ynn_39428/01_2025/8ynn_39428.map" model { file = "/net/cci-nas-00/data/ceres_data/8ynn_39428/01_2025/8ynn_39428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ynn_39428/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.63, per 1000 atoms: 0.66 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: 2.91 Conformation dependent library (CDL) restraints added in 1.2 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: 0.96 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: 2.48 Time building geometry restraints manager: 3.26 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.520 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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= 0.174 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 *********************** 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 : 1.270 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: 0.2213 time to fit residues: 83.1011 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 : 1.589 ------------------------------------------------------------------------------- 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 = 66159.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042866 restraints weight = 40061.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043257 restraints weight = 30109.045| |-----------------------------------------------------------------------------| 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= 0.221 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 *********************** 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 : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.9306 (tt0) cc_final: 0.9010 (tm-30) REVERT: A 46 GLN cc_start: 0.9499 (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: 0.8980 (mt0) REVERT: B 86 MET cc_start: 0.8877 (tpp) cc_final: 0.8648 (tpp) REVERT: B 104 MET cc_start: 0.8865 (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: 0.9015 (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: 0.7499 (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: 0.8537 (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: 0.8876 (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: 0.2047 time to fit residues: 55.9157 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 : 1.336 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.055895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041391 restraints weight = 67322.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.042557 restraints weight = 43032.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043364 restraints weight = 32171.710| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10224 Z= 0.177 Angle : 0.599 11.920 13693 Z= 0.298 Chirality : 0.038 0.185 1588 Planarity : 0.003 0.036 1742 Dihedral : 3.643 15.411 1348 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.13 % Allowed : 12.23 % Favored : 86.64 % 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: 1.50 (0.25), residues: 1212 helix: 1.49 (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 H 88 PHE 0.026 0.002 PHE C 181 TYR 0.019 0.001 TYR H 60 ARG 0.003 0.000 ARG C 47 *********************** 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 170 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.279 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: 0.9283 (tt0) cc_final: 0.8994 (tm-30) REVERT: A 35 GLN cc_start: 0.9074 (tt0) cc_final: 0.8628 (tm-30) REVERT: A 46 GLN cc_start: 0.9523 (mt0) cc_final: 0.9138 (tm-30) REVERT: B 46 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8236 (tm-30) REVERT: B 49 GLN cc_start: 0.9265 (mt0) cc_final: 0.8946 (mt0) REVERT: B 86 MET cc_start: 0.8848 (tpp) cc_final: 0.8563 (tpp) REVERT: B 104 MET cc_start: 0.8910 (ptm) cc_final: 0.8599 (ptm) REVERT: C 43 MET cc_start: 0.9323 (mmm) cc_final: 0.9058 (mmm) REVERT: C 45 PHE cc_start: 0.9577 (m-10) cc_final: 0.9236 (m-80) REVERT: H 20 MET cc_start: 0.9606 (ttm) cc_final: 0.9323 (tpp) REVERT: H 36 ASN cc_start: 0.7147 (t0) cc_final: 0.6887 (t0) REVERT: I 16 ASP cc_start: 0.9457 (t70) cc_final: 0.9252 (p0) REVERT: I 17 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8910 (mt-10) REVERT: I 30 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7509 (mm) REVERT: I 97 MET cc_start: 0.9721 (mmp) cc_final: 0.9465 (mmm) REVERT: I 116 MET cc_start: 0.9322 (mmm) cc_final: 0.9093 (mmm) REVERT: J 1 MET cc_start: 0.8438 (pmm) cc_final: 0.8108 (pmm) REVERT: J 17 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8533 (mt-10) REVERT: J 25 CYS cc_start: 0.9589 (m) cc_final: 0.9198 (p) REVERT: J 116 MET cc_start: 0.9447 (mmt) cc_final: 0.8935 (mmm) REVERT: K 20 MET cc_start: 0.9386 (ttt) cc_final: 0.8890 (tpp) REVERT: K 82 HIS cc_start: 0.8757 (t70) cc_final: 0.8346 (t70) REVERT: K 131 PHE cc_start: 0.9128 (t80) cc_final: 0.8870 (t80) outliers start: 13 outliers final: 7 residues processed: 165 average time/residue: 0.1998 time to fit residues: 47.8748 Evaluate side-chains 142 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.054440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039965 restraints weight = 68556.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041023 restraints weight = 44457.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041782 restraints weight = 33661.797| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10224 Z= 0.316 Angle : 0.657 9.709 13693 Z= 0.335 Chirality : 0.039 0.208 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.887 16.424 1348 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 1.26 (0.25), residues: 1212 helix: 1.32 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 160 PHE 0.046 0.002 PHE C 181 TYR 0.027 0.002 TYR B 101 ARG 0.006 0.000 ARG A 88 *********************** 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 165 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.243 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 35 GLN cc_start: 0.9086 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 46 GLN cc_start: 0.9552 (mt0) cc_final: 0.9173 (tm-30) REVERT: B 46 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8279 (tm-30) REVERT: B 86 MET cc_start: 0.8943 (tpp) cc_final: 0.8664 (tpp) REVERT: C 43 MET cc_start: 0.9353 (mmm) cc_final: 0.8800 (mmm) REVERT: C 46 GLN cc_start: 0.9430 (mt0) cc_final: 0.8986 (mp10) REVERT: C 145 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8764 (mt-10) REVERT: H 20 MET cc_start: 0.9618 (ttm) cc_final: 0.9346 (tpp) REVERT: I 17 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8892 (mt-10) REVERT: I 30 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7575 (mm) REVERT: I 97 MET cc_start: 0.9709 (mmp) cc_final: 0.9416 (mmm) REVERT: I 116 MET cc_start: 0.9284 (mmm) cc_final: 0.9031 (mmm) REVERT: J 17 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8580 (mt-10) REVERT: J 25 CYS cc_start: 0.9622 (m) cc_final: 0.9299 (p) REVERT: K 20 MET cc_start: 0.9423 (ttt) cc_final: 0.8918 (tpp) REVERT: K 131 PHE cc_start: 0.9234 (t80) cc_final: 0.8996 (t80) outliers start: 26 outliers final: 16 residues processed: 158 average time/residue: 0.1927 time to fit residues: 45.1879 Evaluate side-chains 150 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 LEU Chi-restraints excluded: chain J residue 68 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 133 ASP 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: 20.0000 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3339 r_free = 0.3339 target = 0.054074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039674 restraints weight = 69041.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040767 restraints weight = 44645.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041505 restraints weight = 33662.204| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10224 Z= 0.310 Angle : 0.658 9.193 13693 Z= 0.330 Chirality : 0.039 0.196 1588 Planarity : 0.003 0.032 1742 Dihedral : 4.053 16.379 1348 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.60 % Allowed : 14.83 % Favored : 82.57 % 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: 1.01 (0.25), residues: 1212 helix: 1.17 (0.18), residues: 956 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 160 PHE 0.043 0.002 PHE C 181 TYR 0.015 0.001 TYR B 101 ARG 0.003 0.000 ARG I 161 *********************** 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: 30 poor density : 134 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9139 (tt0) cc_final: 0.8624 (tm-30) REVERT: A 46 GLN cc_start: 0.9561 (mt0) cc_final: 0.9165 (tm-30) REVERT: B 86 MET cc_start: 0.8907 (tpp) cc_final: 0.8620 (tpp) REVERT: B 104 MET cc_start: 0.8905 (ptm) cc_final: 0.8600 (ptm) REVERT: C 43 MET cc_start: 0.9370 (mmm) cc_final: 0.9089 (mmm) REVERT: H 20 MET cc_start: 0.9612 (ttm) cc_final: 0.9339 (tpp) REVERT: I 17 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8952 (mt-10) REVERT: I 30 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7609 (mm) REVERT: I 68 LEU cc_start: 0.9501 (tp) cc_final: 0.9281 (tt) REVERT: I 97 MET cc_start: 0.9710 (mmp) cc_final: 0.9397 (mmm) REVERT: J 17 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8620 (mt-10) REVERT: J 25 CYS cc_start: 0.9612 (m) cc_final: 0.9316 (p) REVERT: K 20 MET cc_start: 0.9428 (ttt) cc_final: 0.8927 (tpp) REVERT: K 131 PHE cc_start: 0.9251 (t80) cc_final: 0.9012 (t80) outliers start: 30 outliers final: 18 residues processed: 155 average time/residue: 0.1866 time to fit residues: 43.0946 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 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 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: 1.9990 chunk 41 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039868 restraints weight = 68149.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040944 restraints weight = 44152.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041728 restraints weight = 33365.279| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10224 Z= 0.260 Angle : 0.641 9.853 13693 Z= 0.320 Chirality : 0.039 0.185 1588 Planarity : 0.003 0.032 1742 Dihedral : 4.060 15.290 1348 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 2.69 % Allowed : 15.96 % Favored : 81.35 % 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: 1.16 (0.25), residues: 1212 helix: 1.31 (0.18), residues: 938 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 82 PHE 0.044 0.002 PHE C 181 TYR 0.015 0.001 TYR K 93 ARG 0.003 0.000 ARG I 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9118 (tt0) cc_final: 0.8617 (tm-30) REVERT: A 107 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8818 (tm-30) REVERT: B 86 MET cc_start: 0.8899 (tpp) cc_final: 0.8607 (tpp) REVERT: B 104 MET cc_start: 0.8916 (ptm) cc_final: 0.8554 (ptm) REVERT: C 1 MET cc_start: 0.7834 (ptp) cc_final: 0.7595 (ptp) REVERT: C 43 MET cc_start: 0.9360 (mmm) cc_final: 0.8819 (mmm) REVERT: C 46 GLN cc_start: 0.9365 (mt0) cc_final: 0.8974 (mp10) REVERT: C 107 GLN cc_start: 0.9695 (mt0) cc_final: 0.9254 (mt0) REVERT: H 20 MET cc_start: 0.9620 (ttm) cc_final: 0.9350 (tpp) REVERT: I 1 MET cc_start: 0.8342 (ttp) cc_final: 0.7535 (ttp) REVERT: I 17 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9039 (mt-10) REVERT: I 30 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7780 (mm) REVERT: I 97 MET cc_start: 0.9691 (mmp) cc_final: 0.9405 (mmm) REVERT: J 17 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8625 (mt-10) REVERT: J 25 CYS cc_start: 0.9599 (m) cc_final: 0.9291 (p) REVERT: J 116 MET cc_start: 0.9369 (tpp) cc_final: 0.8843 (mmm) REVERT: K 20 MET cc_start: 0.9427 (ttt) cc_final: 0.8926 (tpp) REVERT: K 131 PHE cc_start: 0.9264 (t80) cc_final: 0.9030 (t80) outliers start: 31 outliers final: 19 residues processed: 154 average time/residue: 0.1883 time to fit residues: 43.3482 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 32 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 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 = 0.3359 r_free = 0.3359 target = 0.054865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040413 restraints weight = 68838.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041559 restraints weight = 44147.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042334 restraints weight = 33115.134| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10224 Z= 0.194 Angle : 0.635 11.000 13693 Z= 0.313 Chirality : 0.039 0.308 1588 Planarity : 0.003 0.032 1742 Dihedral : 4.002 19.633 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 1.99 % Allowed : 16.74 % Favored : 81.27 % 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: 1.35 (0.25), residues: 1212 helix: 1.46 (0.18), residues: 938 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 82 PHE 0.044 0.002 PHE C 181 TYR 0.015 0.001 TYR K 93 ARG 0.003 0.000 ARG I 161 *********************** 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 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5988 (ptt) cc_final: 0.5470 (mtm) REVERT: A 35 GLN cc_start: 0.9114 (tt0) cc_final: 0.8588 (tm-30) REVERT: A 46 GLN cc_start: 0.9563 (mt0) cc_final: 0.9166 (tm-30) REVERT: A 146 MET cc_start: 0.9278 (ttp) cc_final: 0.9031 (ppp) REVERT: B 53 MET cc_start: 0.9027 (mtp) cc_final: 0.8819 (mtt) REVERT: B 86 MET cc_start: 0.8889 (tpp) cc_final: 0.8601 (tpp) REVERT: B 104 MET cc_start: 0.8916 (ptm) cc_final: 0.8538 (ptm) REVERT: C 1 MET cc_start: 0.7837 (ptp) cc_final: 0.7503 (ptp) REVERT: C 43 MET cc_start: 0.9351 (mmm) cc_final: 0.8663 (mmm) REVERT: C 45 PHE cc_start: 0.9544 (m-10) cc_final: 0.9207 (m-80) REVERT: C 46 GLN cc_start: 0.9358 (mt0) cc_final: 0.9025 (mt0) REVERT: C 86 MET cc_start: 0.9797 (tpp) cc_final: 0.9518 (tmm) REVERT: C 107 GLN cc_start: 0.9709 (mt0) cc_final: 0.9242 (mt0) REVERT: C 134 ASP cc_start: 0.9402 (t0) cc_final: 0.9126 (t70) REVERT: H 20 MET cc_start: 0.9630 (ttm) cc_final: 0.9358 (tpp) REVERT: I 1 MET cc_start: 0.8343 (ttp) cc_final: 0.7531 (ttp) REVERT: I 17 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9010 (mt-10) REVERT: I 30 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7834 (mm) REVERT: I 97 MET cc_start: 0.9710 (mmp) cc_final: 0.9345 (mmm) REVERT: J 17 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8595 (mt-10) REVERT: J 25 CYS cc_start: 0.9605 (m) cc_final: 0.9273 (p) REVERT: J 116 MET cc_start: 0.9380 (tpp) cc_final: 0.8930 (mmm) REVERT: K 1 MET cc_start: 0.7342 (ptm) cc_final: 0.7066 (ttt) REVERT: K 20 MET cc_start: 0.9413 (ttt) cc_final: 0.8873 (tpp) REVERT: K 131 PHE cc_start: 0.9273 (t80) cc_final: 0.9054 (t80) outliers start: 23 outliers final: 20 residues processed: 153 average time/residue: 0.1914 time to fit residues: 43.4654 Evaluate side-chains 150 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 83 LEU 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 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 Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.055179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040734 restraints weight = 67948.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041887 restraints weight = 43572.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042665 restraints weight = 32670.921| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10224 Z= 0.191 Angle : 0.633 11.639 13693 Z= 0.311 Chirality : 0.039 0.285 1588 Planarity : 0.003 0.031 1742 Dihedral : 3.905 14.334 1348 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 2.43 % Allowed : 16.91 % Favored : 80.66 % 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: 1.37 (0.25), residues: 1212 helix: 1.47 (0.18), residues: 937 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 82 PHE 0.043 0.002 PHE C 181 TYR 0.016 0.001 TYR K 93 ARG 0.003 0.000 ARG I 161 *********************** 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 160 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5912 (ptt) cc_final: 0.5637 (mtm) REVERT: A 35 GLN cc_start: 0.9070 (tt0) cc_final: 0.8508 (tm-30) REVERT: A 46 GLN cc_start: 0.9569 (mt0) cc_final: 0.9159 (tm-30) REVERT: A 146 MET cc_start: 0.9278 (ttp) cc_final: 0.9048 (ppp) REVERT: B 46 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8209 (tm-30) REVERT: B 53 MET cc_start: 0.9020 (mtp) cc_final: 0.8812 (mtt) REVERT: B 86 MET cc_start: 0.8935 (tpp) cc_final: 0.8640 (tpp) REVERT: B 104 MET cc_start: 0.8970 (ptm) cc_final: 0.8579 (ptm) REVERT: C 1 MET cc_start: 0.7766 (ptp) cc_final: 0.7457 (ptp) REVERT: C 43 MET cc_start: 0.9357 (mmm) cc_final: 0.8701 (mmm) REVERT: C 45 PHE cc_start: 0.9563 (m-10) cc_final: 0.9237 (m-80) REVERT: C 46 GLN cc_start: 0.9333 (mt0) cc_final: 0.8938 (mt0) REVERT: C 86 MET cc_start: 0.9784 (tpp) cc_final: 0.9477 (tmm) REVERT: C 107 GLN cc_start: 0.9713 (mt0) cc_final: 0.9249 (mt0) REVERT: C 137 MET cc_start: 0.8507 (ptp) cc_final: 0.7812 (pmm) REVERT: H 20 MET cc_start: 0.9634 (ttm) cc_final: 0.9355 (tpp) REVERT: I 1 MET cc_start: 0.8358 (ttp) cc_final: 0.7545 (ttp) REVERT: I 17 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9024 (mt-10) REVERT: I 30 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7857 (mm) REVERT: I 97 MET cc_start: 0.9692 (mmp) cc_final: 0.9326 (mmm) REVERT: J 17 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8546 (mt-10) REVERT: J 25 CYS cc_start: 0.9602 (m) cc_final: 0.9250 (p) REVERT: J 116 MET cc_start: 0.9406 (tpp) cc_final: 0.8998 (mmm) REVERT: K 1 MET cc_start: 0.7303 (ptm) cc_final: 0.6943 (ttt) REVERT: K 20 MET cc_start: 0.9375 (ttt) cc_final: 0.8931 (tpp) REVERT: K 131 PHE cc_start: 0.9307 (t80) cc_final: 0.9104 (t80) outliers start: 28 outliers final: 19 residues processed: 151 average time/residue: 0.1843 time to fit residues: 41.6032 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 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 13 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 83 LEU 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 22 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 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 = 0.3372 r_free = 0.3372 target = 0.055295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040848 restraints weight = 67905.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042000 restraints weight = 43599.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042775 restraints weight = 32689.686| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4258 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= 0.180 Angle : 0.641 11.478 13693 Z= 0.313 Chirality : 0.039 0.286 1588 Planarity : 0.003 0.035 1742 Dihedral : 3.909 23.716 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 2.25 % Allowed : 16.65 % 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 : -0.94 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 82 PHE 0.048 0.002 PHE C 181 TYR 0.022 0.001 TYR A 8 ARG 0.003 0.000 ARG I 161 *********************** 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 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.228 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: 0.9066 (tt0) cc_final: 0.8501 (tm-30) REVERT: A 46 GLN cc_start: 0.9567 (mt0) cc_final: 0.9168 (tm-30) REVERT: A 108 ILE cc_start: 0.9663 (mt) cc_final: 0.9382 (mm) REVERT: A 181 PHE cc_start: 0.8637 (m-10) cc_final: 0.8410 (m-80) REVERT: B 46 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8148 (tm-30) REVERT: B 53 MET cc_start: 0.9009 (mtp) cc_final: 0.8783 (mtt) REVERT: B 86 MET cc_start: 0.8921 (tpp) cc_final: 0.8625 (tpp) REVERT: B 104 MET cc_start: 0.8932 (ptm) cc_final: 0.8576 (ptm) REVERT: C 43 MET cc_start: 0.9351 (mmm) cc_final: 0.8672 (mmm) REVERT: C 45 PHE cc_start: 0.9572 (m-10) cc_final: 0.9236 (m-80) REVERT: C 46 GLN cc_start: 0.9300 (mt0) cc_final: 0.9047 (mt0) REVERT: C 86 MET cc_start: 0.9776 (tpp) cc_final: 0.9476 (tmm) REVERT: C 107 GLN cc_start: 0.9713 (mt0) cc_final: 0.9238 (mt0) REVERT: C 137 MET cc_start: 0.8450 (ptp) cc_final: 0.7775 (pmm) REVERT: H 20 MET cc_start: 0.9624 (ttm) cc_final: 0.9349 (tpp) REVERT: I 1 MET cc_start: 0.8392 (ttp) cc_final: 0.7577 (ttp) REVERT: I 17 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9029 (mt-10) REVERT: I 30 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7850 (mm) REVERT: I 97 MET cc_start: 0.9692 (mmp) cc_final: 0.9321 (mmm) REVERT: J 17 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8552 (mt-10) REVERT: J 25 CYS cc_start: 0.9589 (m) cc_final: 0.9214 (p) REVERT: J 116 MET cc_start: 0.9415 (tpp) cc_final: 0.9052 (mmm) REVERT: K 1 MET cc_start: 0.7336 (ptm) cc_final: 0.6989 (ttt) REVERT: K 20 MET cc_start: 0.9375 (ttt) cc_final: 0.8932 (tpp) outliers start: 26 outliers final: 17 residues processed: 153 average time/residue: 0.1908 time to fit residues: 43.1975 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 32 GLN 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 13 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.055365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040828 restraints weight = 66677.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042001 restraints weight = 42060.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042833 restraints weight = 31294.354| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10224 Z= 0.174 Angle : 0.681 13.492 13693 Z= 0.326 Chirality : 0.041 0.446 1588 Planarity : 0.003 0.038 1742 Dihedral : 3.899 23.159 1348 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 1.73 % Allowed : 18.21 % Favored : 80.05 % 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: 1.45 (0.18), residues: 943 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS K 82 PHE 0.058 0.002 PHE H 131 TYR 0.013 0.001 TYR K 93 ARG 0.004 0.000 ARG C 47 ********************** 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 159 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9065 (tt0) cc_final: 0.8505 (tm-30) REVERT: A 46 GLN cc_start: 0.9585 (mt0) cc_final: 0.9168 (tm-30) REVERT: A 181 PHE cc_start: 0.8627 (m-10) cc_final: 0.8392 (m-80) REVERT: B 46 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8214 (tm-30) REVERT: B 49 GLN cc_start: 0.9197 (mt0) cc_final: 0.8939 (mt0) REVERT: B 53 MET cc_start: 0.9050 (mtp) cc_final: 0.8822 (mtt) REVERT: B 86 MET cc_start: 0.8977 (tpp) cc_final: 0.8670 (tpp) REVERT: B 104 MET cc_start: 0.8982 (ptm) cc_final: 0.8629 (ptm) REVERT: C 43 MET cc_start: 0.9375 (mmm) cc_final: 0.8707 (mmm) REVERT: C 45 PHE cc_start: 0.9614 (m-10) cc_final: 0.9217 (m-80) REVERT: C 46 GLN cc_start: 0.9426 (mt0) cc_final: 0.8934 (mt0) REVERT: C 53 MET cc_start: 0.8890 (mtm) cc_final: 0.8577 (ttp) REVERT: C 86 MET cc_start: 0.9780 (tpp) cc_final: 0.9476 (tmm) REVERT: H 20 MET cc_start: 0.9629 (ttm) cc_final: 0.9352 (tpp) REVERT: I 1 MET cc_start: 0.8386 (ttp) cc_final: 0.7559 (ttp) REVERT: I 17 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9051 (mt-10) REVERT: I 30 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7865 (mm) REVERT: I 97 MET cc_start: 0.9705 (mmp) cc_final: 0.9302 (mmm) REVERT: J 17 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8572 (mt-10) REVERT: J 21 LEU cc_start: 0.9859 (mt) cc_final: 0.9643 (mt) REVERT: J 25 CYS cc_start: 0.9617 (m) cc_final: 0.9213 (p) REVERT: J 116 MET cc_start: 0.9430 (tpp) cc_final: 0.9100 (mmm) REVERT: K 1 MET cc_start: 0.7367 (ptm) cc_final: 0.6883 (ttt) REVERT: K 20 MET cc_start: 0.9373 (ttt) cc_final: 0.8937 (tpp) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 0.1944 time to fit residues: 43.6747 Evaluate side-chains 148 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 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 22 LEU Chi-restraints excluded: chain K residue 30 ILE 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 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS K 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040822 restraints weight = 67974.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041936 restraints weight = 43832.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042760 restraints weight = 33047.883| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10224 Z= 0.192 Angle : 0.700 12.713 13693 Z= 0.331 Chirality : 0.041 0.418 1588 Planarity : 0.003 0.041 1742 Dihedral : 3.972 25.128 1348 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 1.82 % Allowed : 18.13 % Favored : 80.05 % 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: 1.35 (0.26), residues: 1212 helix: 1.44 (0.18), residues: 943 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 82 PHE 0.049 0.002 PHE C 181 TYR 0.017 0.001 TYR A 8 ARG 0.003 0.000 ARG I 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.12 seconds wall clock time: 52 minutes 44.05 seconds (3164.05 seconds total)