Starting phenix.real_space_refine on Sun Nov 17 11:57:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_39428.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_39428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_39428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_39428.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ynn_39428/11_2024/8ynn_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-5513/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: 6.91, per 1000 atoms: 0.68 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: 2.60 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: 0.91 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: 2.36 Time building geometry restraints manager: 2.99 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.650 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- 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: 0.2166 time to fit residues: 81.2659 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 : 1.361 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 1.271 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 13 GLN cc_start: 0.9503 (mm-40) cc_final: 0.9228 (mm-40) REVERT: A 17 GLU cc_start: 0.9305 (tt0) cc_final: 0.8967 (tm-30) REVERT: A 46 GLN cc_start: 0.9498 (mt0) cc_final: 0.9079 (tm-30) REVERT: A 104 MET cc_start: 0.9219 (tmm) cc_final: 0.8971 (ppp) REVERT: A 105 LEU cc_start: 0.9675 (mt) cc_final: 0.9417 (mt) REVERT: B 43 MET cc_start: 0.8569 (mmm) cc_final: 0.8325 (mmm) REVERT: B 46 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8260 (tm-30) REVERT: B 49 GLN cc_start: 0.9326 (mt0) cc_final: 0.8938 (mt0) REVERT: B 86 MET cc_start: 0.8606 (tpp) cc_final: 0.8398 (tpp) REVERT: B 104 MET cc_start: 0.8082 (ptm) cc_final: 0.7876 (ptm) REVERT: B 152 LEU cc_start: 0.9584 (tp) cc_final: 0.9150 (mt) REVERT: C 43 MET cc_start: 0.9229 (mmm) cc_final: 0.8954 (mmm) REVERT: C 45 PHE cc_start: 0.9602 (m-10) cc_final: 0.9249 (m-80) REVERT: C 49 GLN cc_start: 0.9429 (mt0) cc_final: 0.9215 (mm110) REVERT: C 107 GLN cc_start: 0.9660 (mt0) cc_final: 0.9274 (mt0) REVERT: H 20 MET cc_start: 0.9615 (ttm) cc_final: 0.9298 (tpp) REVERT: I 16 ASP cc_start: 0.9411 (t70) cc_final: 0.9200 (p0) REVERT: I 17 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8927 (mt-10) REVERT: I 30 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7386 (mm) REVERT: I 116 MET cc_start: 0.9358 (mmm) cc_final: 0.9072 (mmm) REVERT: J 1 MET cc_start: 0.8615 (pmm) cc_final: 0.8357 (pmm) REVERT: J 17 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8501 (mt-10) REVERT: J 25 CYS cc_start: 0.9593 (m) cc_final: 0.9238 (p) REVERT: J 116 MET cc_start: 0.9447 (mmt) cc_final: 0.9017 (mmm) REVERT: K 20 MET cc_start: 0.9434 (ttt) cc_final: 0.8863 (tpp) REVERT: K 82 HIS cc_start: 0.8730 (t70) cc_final: 0.8345 (t70) REVERT: K 86 ASN cc_start: 0.7227 (m110) cc_final: 0.7010 (m110) REVERT: K 131 PHE cc_start: 0.8936 (t80) cc_final: 0.8466 (t80) outliers start: 20 outliers final: 5 residues processed: 189 average time/residue: 0.2003 time to fit residues: 54.5243 Evaluate side-chains 147 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10224 Z= 0.160 Angle : 0.592 12.206 13693 Z= 0.294 Chirality : 0.037 0.175 1588 Planarity : 0.003 0.036 1742 Dihedral : 3.608 15.281 1348 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 12.32 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1212 helix: 1.49 (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 0.002 0.000 HIS H 88 PHE 0.028 0.002 PHE C 181 TYR 0.020 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 177 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.253 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 13 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9235 (mm-40) REVERT: A 17 GLU cc_start: 0.9262 (tt0) cc_final: 0.8937 (tm-30) REVERT: A 35 GLN cc_start: 0.8970 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 46 GLN cc_start: 0.9510 (mt0) cc_final: 0.9102 (tm-30) REVERT: A 104 MET cc_start: 0.9230 (tmm) cc_final: 0.8888 (tmm) REVERT: A 105 LEU cc_start: 0.9686 (mt) cc_final: 0.9321 (mt) REVERT: B 43 MET cc_start: 0.8588 (mmm) cc_final: 0.8372 (mmm) REVERT: B 46 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8310 (tm-30) REVERT: B 49 GLN cc_start: 0.9277 (mt0) cc_final: 0.8927 (mt0) REVERT: B 86 MET cc_start: 0.8575 (tpp) cc_final: 0.8322 (tpp) REVERT: B 104 MET cc_start: 0.8191 (ptm) cc_final: 0.7848 (ptm) REVERT: C 32 GLN cc_start: 0.9284 (mm110) cc_final: 0.8854 (mm-40) REVERT: C 43 MET cc_start: 0.9269 (mmm) cc_final: 0.9013 (mmm) REVERT: C 45 PHE cc_start: 0.9604 (m-10) cc_final: 0.9249 (m-80) REVERT: H 20 MET cc_start: 0.9618 (ttm) cc_final: 0.9341 (tpp) REVERT: H 36 ASN cc_start: 0.7162 (t0) cc_final: 0.6912 (t0) REVERT: I 17 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8899 (mt-10) REVERT: I 30 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7464 (mm) REVERT: I 116 MET cc_start: 0.9333 (mmm) cc_final: 0.9113 (mmm) REVERT: J 1 MET cc_start: 0.8447 (pmm) cc_final: 0.8092 (pmm) REVERT: J 17 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8488 (mt-10) REVERT: J 25 CYS cc_start: 0.9543 (m) cc_final: 0.9170 (p) REVERT: J 116 MET cc_start: 0.9406 (mmt) cc_final: 0.8949 (mmm) REVERT: K 20 MET cc_start: 0.9381 (ttt) cc_final: 0.8784 (tpt) REVERT: K 82 HIS cc_start: 0.8747 (t70) cc_final: 0.8322 (t70) REVERT: K 131 PHE cc_start: 0.9036 (t80) cc_final: 0.8833 (t80) outliers start: 14 outliers final: 7 residues processed: 173 average time/residue: 0.2017 time to fit residues: 50.3498 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 83 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 160 HIS J 82 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10224 Z= 0.437 Angle : 0.759 8.330 13693 Z= 0.387 Chirality : 0.041 0.133 1588 Planarity : 0.004 0.049 1742 Dihedral : 4.120 16.305 1348 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.43 % Allowed : 13.44 % Favored : 84.13 % 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: 0.86 (0.25), residues: 1212 helix: 1.02 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -1.00 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 160 PHE 0.046 0.003 PHE C 181 TYR 0.027 0.002 TYR B 101 ARG 0.006 0.001 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 162 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.443 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 13 GLN cc_start: 0.9535 (mm-40) cc_final: 0.9268 (mp10) REVERT: A 46 GLN cc_start: 0.9543 (mt0) cc_final: 0.9134 (tm-30) REVERT: A 105 LEU cc_start: 0.9685 (mt) cc_final: 0.9388 (mt) REVERT: B 43 MET cc_start: 0.8715 (mmm) cc_final: 0.8465 (mmm) REVERT: B 86 MET cc_start: 0.8732 (tpp) cc_final: 0.8501 (tpp) REVERT: C 43 MET cc_start: 0.9339 (mmm) cc_final: 0.9052 (mmm) REVERT: C 145 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8742 (mt-10) REVERT: H 20 MET cc_start: 0.9621 (ttm) cc_final: 0.9358 (tpp) REVERT: H 116 MET cc_start: 0.8724 (mmt) cc_final: 0.8515 (mmt) REVERT: I 17 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8970 (mt-10) REVERT: I 97 MET cc_start: 0.9643 (mmm) cc_final: 0.9415 (mmm) REVERT: J 25 CYS cc_start: 0.9584 (m) cc_final: 0.9353 (p) REVERT: K 20 MET cc_start: 0.9439 (ttt) cc_final: 0.8949 (tpp) REVERT: K 131 PHE cc_start: 0.9179 (t80) cc_final: 0.8973 (t80) outliers start: 28 outliers final: 19 residues processed: 156 average time/residue: 0.1810 time to fit residues: 42.8738 Evaluate side-chains 146 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 30 ILE 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 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: 0.0980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10224 Z= 0.156 Angle : 0.611 11.305 13693 Z= 0.300 Chirality : 0.038 0.200 1588 Planarity : 0.003 0.032 1742 Dihedral : 3.804 16.021 1348 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.91 % Allowed : 14.92 % Favored : 83.17 % 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: 1.30 (0.25), residues: 1212 helix: 1.36 (0.18), residues: 965 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 82 PHE 0.042 0.002 PHE C 181 TYR 0.014 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 177 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.380 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 13 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9197 (mm-40) REVERT: A 35 GLN cc_start: 0.8860 (tt0) cc_final: 0.8623 (tm-30) REVERT: A 46 GLN cc_start: 0.9536 (mt0) cc_final: 0.9115 (tm-30) REVERT: A 104 MET cc_start: 0.9116 (tmm) cc_final: 0.8730 (ppp) REVERT: A 105 LEU cc_start: 0.9654 (mt) cc_final: 0.9432 (mt) REVERT: B 43 MET cc_start: 0.8688 (mmm) cc_final: 0.8415 (mmm) REVERT: B 46 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8243 (tm-30) REVERT: B 49 GLN cc_start: 0.9246 (mt0) cc_final: 0.8880 (mt0) REVERT: B 86 MET cc_start: 0.8579 (tpp) cc_final: 0.8309 (tpp) REVERT: B 104 MET cc_start: 0.8578 (ptm) cc_final: 0.8208 (ptm) REVERT: C 43 MET cc_start: 0.9309 (mmm) cc_final: 0.9057 (mmm) REVERT: C 45 PHE cc_start: 0.9592 (m-10) cc_final: 0.9169 (m-80) REVERT: C 107 GLN cc_start: 0.9670 (mt0) cc_final: 0.9248 (mt0) REVERT: H 20 MET cc_start: 0.9621 (ttm) cc_final: 0.9349 (tpp) REVERT: I 1 MET cc_start: 0.8487 (ttp) cc_final: 0.7570 (ttp) REVERT: I 17 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9028 (mt-10) REVERT: I 30 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7592 (mm) REVERT: I 97 MET cc_start: 0.9598 (mmm) cc_final: 0.9366 (mmm) REVERT: J 17 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8502 (mt-10) REVERT: J 25 CYS cc_start: 0.9539 (m) cc_final: 0.9213 (p) REVERT: J 116 MET cc_start: 0.9321 (tpp) cc_final: 0.8663 (mmm) REVERT: K 20 MET cc_start: 0.9423 (ttt) cc_final: 0.8941 (tpp) REVERT: K 21 LEU cc_start: 0.9749 (tp) cc_final: 0.9499 (pp) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 0.1794 time to fit residues: 46.0617 Evaluate side-chains 151 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10224 Z= 0.248 Angle : 0.633 10.745 13693 Z= 0.315 Chirality : 0.038 0.177 1588 Planarity : 0.003 0.032 1742 Dihedral : 3.940 17.162 1348 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 2.34 % Allowed : 16.05 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1212 helix: 1.46 (0.18), residues: 947 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 82 PHE 0.043 0.002 PHE C 181 TYR 0.018 0.001 TYR K 93 ARG 0.004 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 163 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.236 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 13 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9257 (mm-40) REVERT: A 35 GLN cc_start: 0.9014 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 46 GLN cc_start: 0.9540 (mt0) cc_final: 0.9122 (tm-30) REVERT: A 104 MET cc_start: 0.9145 (tmm) cc_final: 0.8732 (ppp) REVERT: A 105 LEU cc_start: 0.9654 (mt) cc_final: 0.9399 (mt) REVERT: B 43 MET cc_start: 0.8739 (mmm) cc_final: 0.8444 (mmm) REVERT: B 46 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8283 (tm-30) REVERT: B 86 MET cc_start: 0.8675 (tpp) cc_final: 0.8421 (tpp) REVERT: B 104 MET cc_start: 0.8517 (ptm) cc_final: 0.8164 (ptm) REVERT: C 1 MET cc_start: 0.7636 (ptp) cc_final: 0.7367 (ptp) REVERT: C 43 MET cc_start: 0.9332 (mmm) cc_final: 0.8735 (mmm) REVERT: C 46 GLN cc_start: 0.9388 (mt0) cc_final: 0.9022 (mp10) REVERT: H 20 MET cc_start: 0.9628 (ttm) cc_final: 0.9353 (tpp) REVERT: H 74 MET cc_start: 0.8753 (ptp) cc_final: 0.8547 (ptp) REVERT: I 1 MET cc_start: 0.8448 (ttp) cc_final: 0.7551 (ttp) REVERT: I 17 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9047 (mt-10) REVERT: I 30 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7639 (mm) REVERT: I 59 LEU cc_start: 0.9687 (mp) cc_final: 0.9287 (tt) REVERT: I 97 MET cc_start: 0.9640 (mmm) cc_final: 0.9403 (mmm) REVERT: J 17 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8573 (mt-10) REVERT: J 25 CYS cc_start: 0.9573 (m) cc_final: 0.9282 (p) REVERT: K 20 MET cc_start: 0.9416 (ttt) cc_final: 0.8934 (tpp) REVERT: K 152 LEU cc_start: 0.9665 (mp) cc_final: 0.9361 (tt) outliers start: 27 outliers final: 18 residues processed: 154 average time/residue: 0.1806 time to fit residues: 42.1130 Evaluate side-chains 154 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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 27 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 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 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4049 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= 0.187 Angle : 0.627 11.533 13693 Z= 0.306 Chirality : 0.037 0.157 1588 Planarity : 0.003 0.031 1742 Dihedral : 3.877 18.156 1348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 1.82 % Allowed : 16.91 % 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: 1.49 (0.26), residues: 1212 helix: 1.53 (0.18), residues: 944 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 82 PHE 0.046 0.002 PHE C 181 TYR 0.012 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: 21 poor density : 141 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5754 (ptt) cc_final: 0.5535 (mtm) REVERT: A 13 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9230 (mm-40) REVERT: A 35 GLN cc_start: 0.9013 (tt0) cc_final: 0.8590 (tm-30) REVERT: A 46 GLN cc_start: 0.9541 (mt0) cc_final: 0.9103 (tm-30) REVERT: A 104 MET cc_start: 0.9064 (tmm) cc_final: 0.8731 (tmm) REVERT: A 105 LEU cc_start: 0.9648 (mt) cc_final: 0.9336 (mt) REVERT: B 43 MET cc_start: 0.8736 (mmm) cc_final: 0.8454 (mmm) REVERT: B 46 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8243 (tm-30) REVERT: B 53 MET cc_start: 0.7787 (mtp) cc_final: 0.7567 (mtt) REVERT: B 86 MET cc_start: 0.8649 (tpp) cc_final: 0.8381 (tpp) REVERT: B 104 MET cc_start: 0.8470 (ptm) cc_final: 0.8159 (ptm) REVERT: C 1 MET cc_start: 0.7729 (ptp) cc_final: 0.7429 (ptp) REVERT: C 43 MET cc_start: 0.9329 (mmm) cc_final: 0.8641 (mmm) REVERT: C 45 PHE cc_start: 0.9411 (m-10) cc_final: 0.9156 (m-80) REVERT: C 46 GLN cc_start: 0.9406 (mt0) cc_final: 0.9061 (mt0) REVERT: C 107 GLN cc_start: 0.9696 (mt0) cc_final: 0.9239 (mt0) REVERT: H 20 MET cc_start: 0.9633 (ttm) cc_final: 0.9362 (tpp) REVERT: H 74 MET cc_start: 0.8742 (ptp) cc_final: 0.8515 (ptp) REVERT: H 120 MET cc_start: 0.7752 (tpp) cc_final: 0.7521 (tpp) REVERT: I 1 MET cc_start: 0.8527 (ttp) cc_final: 0.7629 (ttp) REVERT: I 17 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9040 (mt-10) REVERT: I 30 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7690 (mm) REVERT: I 97 MET cc_start: 0.9623 (mmm) cc_final: 0.9382 (mmm) REVERT: J 17 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8540 (mt-10) REVERT: J 25 CYS cc_start: 0.9569 (m) cc_final: 0.9258 (p) REVERT: J 116 MET cc_start: 0.9361 (tpp) cc_final: 0.9103 (mmm) REVERT: K 20 MET cc_start: 0.9400 (ttt) cc_final: 0.8968 (tpp) REVERT: K 21 LEU cc_start: 0.9752 (tp) cc_final: 0.9474 (pp) outliers start: 21 outliers final: 17 residues processed: 155 average time/residue: 0.1829 time to fit residues: 42.5449 Evaluate side-chains 152 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 32 GLN 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 27 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4189 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= 0.163 Angle : 0.622 12.317 13693 Z= 0.304 Chirality : 0.037 0.234 1588 Planarity : 0.003 0.030 1742 Dihedral : 3.805 19.286 1348 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 2.08 % Allowed : 17.52 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.26), residues: 1212 helix: 1.52 (0.18), residues: 944 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 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 70 *********************** 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 167 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9223 (mm-40) REVERT: A 35 GLN cc_start: 0.8940 (tt0) cc_final: 0.8502 (tm-30) REVERT: A 46 GLN cc_start: 0.9541 (mt0) cc_final: 0.9103 (tm-30) REVERT: A 104 MET cc_start: 0.9127 (tmm) cc_final: 0.8753 (tmm) REVERT: A 105 LEU cc_start: 0.9625 (mt) cc_final: 0.9282 (mt) REVERT: A 181 PHE cc_start: 0.8566 (m-10) cc_final: 0.8358 (m-80) REVERT: B 43 MET cc_start: 0.8734 (mmm) cc_final: 0.8470 (mmm) REVERT: B 46 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8276 (tm-30) REVERT: B 49 GLN cc_start: 0.9186 (mt0) cc_final: 0.8878 (mt0) REVERT: B 53 MET cc_start: 0.7770 (mtp) cc_final: 0.7516 (mtt) REVERT: B 86 MET cc_start: 0.8630 (tpp) cc_final: 0.8363 (tpp) REVERT: B 104 MET cc_start: 0.8473 (ptm) cc_final: 0.8133 (ptm) REVERT: C 43 MET cc_start: 0.9322 (mmm) cc_final: 0.8585 (mmm) REVERT: C 46 GLN cc_start: 0.9400 (mt0) cc_final: 0.9052 (mt0) REVERT: H 20 MET cc_start: 0.9624 (ttm) cc_final: 0.9359 (tpp) REVERT: H 74 MET cc_start: 0.8728 (ptp) cc_final: 0.8487 (ptp) REVERT: H 120 MET cc_start: 0.8016 (tpp) cc_final: 0.7808 (tpp) REVERT: I 1 MET cc_start: 0.8545 (ttp) cc_final: 0.7636 (ttp) REVERT: I 17 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9045 (mt-10) REVERT: I 30 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7753 (mm) REVERT: I 68 LEU cc_start: 0.9258 (tt) cc_final: 0.8929 (pp) REVERT: I 97 MET cc_start: 0.9603 (mmm) cc_final: 0.9363 (mmm) REVERT: J 17 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8517 (mt-10) REVERT: J 25 CYS cc_start: 0.9563 (m) cc_final: 0.9214 (p) REVERT: J 116 MET cc_start: 0.9374 (tpp) cc_final: 0.9047 (mmm) REVERT: K 20 MET cc_start: 0.9390 (ttt) cc_final: 0.8985 (tpp) REVERT: K 21 LEU cc_start: 0.9753 (tp) cc_final: 0.9466 (pp) outliers start: 24 outliers final: 14 residues processed: 159 average time/residue: 0.1780 time to fit residues: 42.6410 Evaluate side-chains 149 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 115 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10224 Z= 0.172 Angle : 0.636 12.527 13693 Z= 0.310 Chirality : 0.037 0.235 1588 Planarity : 0.003 0.035 1742 Dihedral : 3.809 19.183 1348 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.99 % Allowed : 17.35 % 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: 1.48 (0.25), residues: 1212 helix: 1.56 (0.18), residues: 940 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS K 82 PHE 0.047 0.002 PHE C 181 TYR 0.016 0.001 TYR B 106 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 160 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.9715 (t80) cc_final: 0.9507 (t80) REVERT: A 13 GLN cc_start: 0.9475 (mm-40) cc_final: 0.9166 (mm-40) REVERT: A 35 GLN cc_start: 0.8980 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 46 GLN cc_start: 0.9544 (mt0) cc_final: 0.9114 (tm-30) REVERT: A 104 MET cc_start: 0.9120 (tmm) cc_final: 0.8751 (tmm) REVERT: A 105 LEU cc_start: 0.9611 (mt) cc_final: 0.9259 (mt) REVERT: A 181 PHE cc_start: 0.8599 (m-10) cc_final: 0.8384 (m-80) REVERT: B 43 MET cc_start: 0.8775 (mmm) cc_final: 0.8501 (mmm) REVERT: B 46 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8250 (tm-30) REVERT: B 49 GLN cc_start: 0.9194 (mt0) cc_final: 0.8892 (mt0) REVERT: B 53 MET cc_start: 0.7764 (mtp) cc_final: 0.7507 (mtt) REVERT: B 86 MET cc_start: 0.8667 (tpp) cc_final: 0.8394 (tpp) REVERT: B 104 MET cc_start: 0.8503 (ptm) cc_final: 0.8166 (ptm) REVERT: C 43 MET cc_start: 0.9324 (mmm) cc_final: 0.8643 (mmm) REVERT: C 45 PHE cc_start: 0.9552 (m-10) cc_final: 0.9210 (m-80) REVERT: C 46 GLN cc_start: 0.9448 (mt0) cc_final: 0.9061 (mt0) REVERT: H 20 MET cc_start: 0.9626 (ttm) cc_final: 0.9359 (tpp) REVERT: H 74 MET cc_start: 0.8713 (ptp) cc_final: 0.8482 (ptp) REVERT: H 104 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.7921 (pp) REVERT: H 120 MET cc_start: 0.8050 (tpp) cc_final: 0.7824 (tpp) REVERT: I 1 MET cc_start: 0.8568 (ttp) cc_final: 0.7670 (ttp) REVERT: I 17 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9042 (mt-10) REVERT: I 30 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7763 (mm) REVERT: I 68 LEU cc_start: 0.9270 (tt) cc_final: 0.8953 (pp) REVERT: I 97 MET cc_start: 0.9593 (mmm) cc_final: 0.9352 (mmm) REVERT: J 17 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8531 (mt-10) REVERT: J 25 CYS cc_start: 0.9569 (m) cc_final: 0.9226 (p) REVERT: J 116 MET cc_start: 0.9370 (tpp) cc_final: 0.9049 (mmm) REVERT: K 20 MET cc_start: 0.9380 (ttt) cc_final: 0.8982 (tpp) REVERT: K 21 LEU cc_start: 0.9754 (tp) cc_final: 0.9463 (pp) outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 0.1863 time to fit residues: 43.1174 Evaluate side-chains 152 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 27 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain H residue 104 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 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 70 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4388 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= 0.175 Angle : 0.665 12.814 13693 Z= 0.323 Chirality : 0.040 0.458 1588 Planarity : 0.003 0.043 1742 Dihedral : 3.843 19.120 1348 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 17.52 % 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: 1.46 (0.26), residues: 1212 helix: 1.54 (0.18), residues: 940 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS K 82 PHE 0.049 0.002 PHE C 181 TYR 0.015 0.001 TYR B 106 ARG 0.003 0.000 ARG I 161 ********************** 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: 21 poor density : 138 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.9722 (t80) cc_final: 0.9507 (t80) REVERT: A 13 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9156 (mm-40) REVERT: A 35 GLN cc_start: 0.8981 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 46 GLN cc_start: 0.9553 (mt0) cc_final: 0.9123 (tm-30) REVERT: A 104 MET cc_start: 0.9096 (tmm) cc_final: 0.8752 (tmm) REVERT: A 105 LEU cc_start: 0.9599 (mt) cc_final: 0.9232 (mt) REVERT: B 43 MET cc_start: 0.8789 (mmm) cc_final: 0.8511 (mmm) REVERT: B 46 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8261 (tm-30) REVERT: B 49 GLN cc_start: 0.9187 (mt0) cc_final: 0.8892 (mt0) REVERT: B 53 MET cc_start: 0.7745 (mtp) cc_final: 0.7488 (mtt) REVERT: B 86 MET cc_start: 0.8666 (tpp) cc_final: 0.8394 (tpp) REVERT: B 104 MET cc_start: 0.8507 (ptm) cc_final: 0.8121 (ptm) REVERT: C 43 MET cc_start: 0.9315 (mmm) cc_final: 0.8622 (mmm) REVERT: C 45 PHE cc_start: 0.9566 (m-10) cc_final: 0.9214 (m-80) REVERT: C 46 GLN cc_start: 0.9407 (mt0) cc_final: 0.9051 (mt0) REVERT: C 137 MET cc_start: 0.8521 (ptp) cc_final: 0.7926 (pmm) REVERT: H 20 MET cc_start: 0.9628 (ttm) cc_final: 0.9353 (tpp) REVERT: H 74 MET cc_start: 0.8695 (ptp) cc_final: 0.8467 (ptp) REVERT: H 104 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.7863 (pp) REVERT: I 1 MET cc_start: 0.8576 (ttp) cc_final: 0.7687 (ttp) REVERT: I 17 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9039 (mt-10) REVERT: I 30 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7779 (mm) REVERT: I 68 LEU cc_start: 0.9270 (tt) cc_final: 0.8972 (pp) REVERT: I 97 MET cc_start: 0.9592 (mmm) cc_final: 0.9344 (mmm) REVERT: J 17 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8520 (mt-10) REVERT: J 25 CYS cc_start: 0.9574 (m) cc_final: 0.9222 (p) REVERT: J 116 MET cc_start: 0.9375 (tpp) cc_final: 0.9076 (mmm) REVERT: K 20 MET cc_start: 0.9378 (ttt) cc_final: 0.8972 (tpp) REVERT: K 21 LEU cc_start: 0.9745 (tp) cc_final: 0.9438 (pp) REVERT: K 40 LEU cc_start: 0.9636 (tt) cc_final: 0.9398 (pp) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.1860 time to fit residues: 42.4436 Evaluate side-chains 155 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 C residue 107 GLN Chi-restraints excluded: chain H residue 104 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 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 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.055359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041194 restraints weight = 65820.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042331 restraints weight = 42850.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043100 restraints weight = 32238.270| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4463 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= 0.194 Angle : 0.672 12.458 13693 Z= 0.326 Chirality : 0.040 0.415 1588 Planarity : 0.003 0.048 1742 Dihedral : 3.864 19.123 1348 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 1.82 % Allowed : 17.87 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1212 helix: 1.51 (0.18), residues: 940 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 82 PHE 0.052 0.002 PHE A 181 TYR 0.012 0.001 TYR K 93 ARG 0.003 0.000 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.68 seconds wall clock time: 37 minutes 41.36 seconds (2261.36 seconds total)