Starting phenix.real_space_refine on Tue Sep 24 12:40:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/09_2024/7ahc_11782.cif" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5288 2.51 5 N 1358 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Time building chain proxies: 5.29, per 1000 atoms: 0.65 Number of scatterers: 8170 At special positions: 0 Unit cell: (94.116, 106.26, 104.236, 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 40 16.00 O 1484 8.00 N 1358 7.00 C 5288 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 68.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.860A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.539A pdb=" N MET A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.948A pdb=" N MET A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 45 removed outlier: 3.861A pdb=" N VAL B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 122 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.538A pdb=" N MET B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 156 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 212 through 232 removed outlier: 3.949A pdb=" N MET B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 276 Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.571A pdb=" N LYS D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 38 removed outlier: 4.094A pdb=" N ILE D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.849A pdb=" N LEU D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.557A pdb=" N THR D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 137 through 153 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.270A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.595A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.566A pdb=" N LYS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 4.088A pdb=" N ILE C 34 " --> pdb=" O PRO C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 4.305A pdb=" N LEU C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.210A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 232 Processing sheet with id=AA1, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.544A pdb=" N ILE D 51 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.232A pdb=" N LEU D 186 " --> pdb=" O ILE D 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.364A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.892A pdb=" N PHE C 220 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 186 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 221 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET C 188 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 475 hydrogen bonds defined for protein. 1377 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: 2.16 Time building geometry restraints manager: 2.54 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: 2624 1.34 - 1.46: 1618 1.46 - 1.58: 3976 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8298 Sorted by residual: bond pdb=" CB VAL A 228 " pdb=" CG2 VAL A 228 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB VAL B 228 " pdb=" CG2 VAL B 228 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB THR A 175 " pdb=" CG2 THR A 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CG LEU A 186 " pdb=" CD1 LEU A 186 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 10840 1.43 - 2.85: 329 2.85 - 4.28: 45 4.28 - 5.70: 6 5.70 - 7.13: 2 Bond angle restraints: 11222 Sorted by residual: angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 112.67 108.99 3.68 1.25e+00 6.40e-01 8.69e+00 angle pdb=" N VAL A 113 " pdb=" CA VAL A 113 " pdb=" C VAL A 113 " ideal model delta sigma weight residual 112.67 109.04 3.63 1.25e+00 6.40e-01 8.45e+00 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 114.04 110.61 3.43 1.24e+00 6.50e-01 7.66e+00 angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 114.04 110.63 3.41 1.24e+00 6.50e-01 7.57e+00 angle pdb=" CA GLY D 61 " pdb=" C GLY D 61 " pdb=" N LEU D 62 " ideal model delta sigma weight residual 114.66 117.19 -2.53 1.10e+00 8.26e-01 5.28e+00 ... (remaining 11217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4414 17.65 - 35.30: 466 35.30 - 52.96: 124 52.96 - 70.61: 22 70.61 - 88.26: 8 Dihedral angle restraints: 5034 sinusoidal: 2008 harmonic: 3026 Sorted by residual: dihedral pdb=" CA MET B 95 " pdb=" C MET B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA MET A 95 " pdb=" C MET A 95 " pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ILE B 128 " pdb=" C ILE B 128 " pdb=" N VAL B 129 " pdb=" CA VAL B 129 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 700 0.027 - 0.054: 370 0.054 - 0.081: 159 0.081 - 0.107: 92 0.107 - 0.134: 39 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL A 164 " pdb=" CA VAL A 164 " pdb=" CG1 VAL A 164 " pdb=" CG2 VAL A 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1357 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 74 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 75 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 136 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 137 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " 0.019 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 280 2.69 - 3.24: 9129 3.24 - 3.80: 12638 3.80 - 4.35: 16891 4.35 - 4.90: 28538 Nonbonded interactions: 67476 Sorted by model distance: nonbonded pdb=" NZ LYS C 242 " pdb=" O ILE C 243 " model vdw 2.141 3.120 nonbonded pdb=" NH2 ARG D 76 " pdb=" OE1 GLU D 79 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS C 6 " pdb=" O ILE C 7 " model vdw 2.225 3.120 nonbonded pdb=" OG SER B 195 " pdb=" OH TYR C 129 " model vdw 2.233 3.040 nonbonded pdb=" NZ LYS D 6 " pdb=" O ILE D 7 " model vdw 2.244 3.120 ... (remaining 67471 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.690 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.008 0.053 8298 Z= 0.493 Angle : 0.609 7.129 11222 Z= 0.346 Chirality : 0.045 0.134 1360 Planarity : 0.004 0.041 1406 Dihedral : 15.793 88.260 3078 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 19.98 % Favored : 79.91 % 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: -4.17 (0.21), residues: 1056 helix: -2.12 (0.17), residues: 654 sheet: -4.79 (0.34), residues: 74 loop : -3.24 (0.27), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 91 HIS 0.003 0.001 HIS D 223 PHE 0.019 0.001 PHE B 135 TYR 0.009 0.001 TYR D 45 ARG 0.002 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8378 (pt) cc_final: 0.7796 (pt) REVERT: B 44 ILE cc_start: 0.8327 (pt) cc_final: 0.7793 (pt) REVERT: C 62 LEU cc_start: 0.8267 (mp) cc_final: 0.7968 (mp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2257 time to fit residues: 49.9855 Evaluate side-chains 104 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 135 ASN D 181 ASN D 215 GLN C 52 ASN C 164 GLN C 170 GLN C 181 ASN C 211 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8298 Z= 0.215 Angle : 0.648 7.670 11222 Z= 0.336 Chirality : 0.045 0.169 1360 Planarity : 0.005 0.043 1406 Dihedral : 5.086 48.514 1114 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.90 % Allowed : 17.52 % Favored : 79.58 % 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: -1.77 (0.26), residues: 1056 helix: -0.28 (0.20), residues: 650 sheet: -3.78 (0.46), residues: 80 loop : -2.08 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 54 HIS 0.001 0.000 HIS D 9 PHE 0.010 0.001 PHE B 77 TYR 0.008 0.001 TYR D 45 ARG 0.003 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7870 (mp) REVERT: B 48 LEU cc_start: 0.3281 (OUTLIER) cc_final: 0.2957 (tt) REVERT: B 177 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7965 (mp) REVERT: D 71 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7969 (mp) outliers start: 26 outliers final: 7 residues processed: 162 average time/residue: 0.1862 time to fit residues: 41.7641 Evaluate side-chains 113 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS C 171 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8298 Z= 0.341 Angle : 0.661 7.814 11222 Z= 0.348 Chirality : 0.047 0.159 1360 Planarity : 0.005 0.047 1406 Dihedral : 5.211 44.230 1114 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.24 % Allowed : 17.52 % Favored : 79.24 % 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 (0.26), residues: 1056 helix: -0.05 (0.20), residues: 658 sheet: -3.16 (0.52), residues: 82 loop : -1.90 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 118 HIS 0.001 0.000 HIS D 223 PHE 0.017 0.002 PHE A 77 TYR 0.008 0.001 TYR D 45 ARG 0.003 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8502 (mp) REVERT: A 177 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 275 LYS cc_start: 0.7986 (mttm) cc_final: 0.7764 (mttm) REVERT: B 107 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 177 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8164 (mp) REVERT: D 71 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7941 (mp) REVERT: D 231 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5132 (tp) REVERT: C 165 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7702 (mp) outliers start: 29 outliers final: 11 residues processed: 167 average time/residue: 0.1861 time to fit residues: 43.2358 Evaluate side-chains 131 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8298 Z= 0.214 Angle : 0.607 8.783 11222 Z= 0.315 Chirality : 0.044 0.183 1360 Planarity : 0.004 0.047 1406 Dihedral : 5.026 41.118 1114 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.79 % Allowed : 18.97 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.26), residues: 1056 helix: 0.30 (0.20), residues: 662 sheet: -2.87 (0.54), residues: 82 loop : -1.73 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 118 HIS 0.001 0.000 HIS C 223 PHE 0.024 0.001 PHE A 53 TYR 0.007 0.001 TYR D 45 ARG 0.003 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.952 Fit side-chains REVERT: A 107 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 174 MET cc_start: 0.8284 (mmm) cc_final: 0.7891 (mmm) REVERT: A 177 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 107 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 174 MET cc_start: 0.8249 (mmm) cc_final: 0.7819 (mmm) REVERT: B 177 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8082 (mp) REVERT: D 71 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7835 (mt) REVERT: D 231 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5128 (tp) REVERT: C 38 THR cc_start: -0.2005 (OUTLIER) cc_final: -0.2426 (m) REVERT: C 165 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7599 (mp) outliers start: 34 outliers final: 17 residues processed: 161 average time/residue: 0.1974 time to fit residues: 43.2489 Evaluate side-chains 142 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.0000 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 130 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 211 GLN C 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8298 Z= 0.176 Angle : 0.581 7.567 11222 Z= 0.300 Chirality : 0.043 0.196 1360 Planarity : 0.004 0.048 1406 Dihedral : 4.897 37.434 1114 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.79 % Allowed : 18.53 % Favored : 77.68 % 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: -0.43 (0.27), residues: 1056 helix: 0.70 (0.21), residues: 654 sheet: -2.62 (0.56), residues: 82 loop : -1.59 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 54 HIS 0.001 0.000 HIS C 223 PHE 0.021 0.001 PHE A 53 TYR 0.005 0.001 TYR C 45 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 177 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 107 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 177 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8105 (mp) REVERT: D 60 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6781 (mmm) REVERT: C 165 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7515 (mp) outliers start: 34 outliers final: 19 residues processed: 162 average time/residue: 0.1906 time to fit residues: 42.4941 Evaluate side-chains 146 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8298 Z= 0.187 Angle : 0.581 7.529 11222 Z= 0.298 Chirality : 0.044 0.214 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.837 33.873 1114 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.24 % Allowed : 20.31 % Favored : 76.45 % 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: -0.31 (0.27), residues: 1056 helix: 0.76 (0.21), residues: 658 sheet: -2.45 (0.56), residues: 82 loop : -1.50 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 118 HIS 0.001 0.000 HIS D 223 PHE 0.019 0.001 PHE A 53 TYR 0.005 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 107 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 139 MET cc_start: 0.7914 (ptp) cc_final: 0.7635 (ptp) REVERT: D 60 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6732 (mmm) REVERT: C 38 THR cc_start: -0.2265 (OUTLIER) cc_final: -0.2649 (m) REVERT: C 165 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7504 (mp) outliers start: 29 outliers final: 19 residues processed: 151 average time/residue: 0.1988 time to fit residues: 41.1151 Evaluate side-chains 142 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.0020 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8298 Z= 0.179 Angle : 0.572 7.488 11222 Z= 0.294 Chirality : 0.043 0.156 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.621 20.250 1110 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.91 % Allowed : 19.75 % Favored : 76.34 % 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: -0.19 (0.27), residues: 1056 helix: 0.82 (0.21), residues: 666 sheet: -2.26 (0.57), residues: 82 loop : -1.47 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 118 HIS 0.001 0.000 HIS D 223 PHE 0.017 0.001 PHE A 53 TYR 0.004 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 177 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8066 (mp) REVERT: B 107 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 177 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8078 (mp) REVERT: D 60 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6654 (mmm) REVERT: C 165 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7512 (mp) outliers start: 35 outliers final: 19 residues processed: 160 average time/residue: 0.1821 time to fit residues: 40.5716 Evaluate side-chains 144 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8298 Z= 0.193 Angle : 0.600 9.178 11222 Z= 0.305 Chirality : 0.043 0.153 1360 Planarity : 0.004 0.048 1406 Dihedral : 4.628 20.132 1110 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.46 % Allowed : 20.65 % Favored : 75.89 % 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: -0.08 (0.27), residues: 1056 helix: 0.93 (0.21), residues: 664 sheet: -2.13 (0.58), residues: 82 loop : -1.50 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 118 HIS 0.001 0.000 HIS C 9 PHE 0.016 0.001 PHE A 53 TYR 0.004 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8589 (t) REVERT: A 107 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 107 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 139 MET cc_start: 0.7917 (ptp) cc_final: 0.7652 (ptp) REVERT: D 60 MET cc_start: 0.7074 (tpp) cc_final: 0.6733 (mmm) REVERT: D 71 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7670 (mt) REVERT: C 165 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7607 (mp) outliers start: 31 outliers final: 18 residues processed: 150 average time/residue: 0.1819 time to fit residues: 38.0810 Evaluate side-chains 143 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8298 Z= 0.242 Angle : 0.627 10.260 11222 Z= 0.317 Chirality : 0.045 0.148 1360 Planarity : 0.004 0.050 1406 Dihedral : 4.719 20.890 1110 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.79 % Allowed : 20.42 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.20 (0.26), residues: 1056 helix: 0.70 (0.20), residues: 678 sheet: -2.04 (0.59), residues: 82 loop : -1.34 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 14 HIS 0.001 0.000 HIS D 223 PHE 0.018 0.001 PHE A 53 TYR 0.006 0.001 TYR D 45 ARG 0.005 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8629 (t) REVERT: A 107 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 107 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 139 MET cc_start: 0.7976 (ptp) cc_final: 0.7692 (ptp) REVERT: B 214 MET cc_start: 0.8009 (mmm) cc_final: 0.7771 (mmp) REVERT: D 60 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6770 (mmm) REVERT: D 71 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7691 (mt) REVERT: C 165 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7559 (mp) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.1851 time to fit residues: 36.3114 Evaluate side-chains 140 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.0020 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8298 Z= 0.187 Angle : 0.626 10.768 11222 Z= 0.311 Chirality : 0.044 0.211 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.661 20.535 1110 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.57 % Allowed : 20.87 % Favored : 76.56 % 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: -0.05 (0.27), residues: 1056 helix: 0.87 (0.20), residues: 666 sheet: -1.92 (0.60), residues: 82 loop : -1.37 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 21 HIS 0.001 0.000 HIS D 223 PHE 0.021 0.001 PHE B 53 TYR 0.004 0.001 TYR C 45 ARG 0.005 0.000 ARG C 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 107 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 107 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 139 MET cc_start: 0.7955 (ptp) cc_final: 0.7676 (ptp) REVERT: B 214 MET cc_start: 0.7989 (mmm) cc_final: 0.7758 (mmp) REVERT: D 60 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6741 (mmm) REVERT: C 165 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7526 (mp) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 0.1768 time to fit residues: 35.4215 Evaluate side-chains 140 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146380 restraints weight = 10233.549| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.68 r_work: 0.3372 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8298 Z= 0.187 Angle : 0.625 10.484 11222 Z= 0.310 Chirality : 0.044 0.246 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.639 20.779 1110 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.68 % Allowed : 20.87 % Favored : 76.45 % 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: 0.01 (0.27), residues: 1056 helix: 0.86 (0.20), residues: 678 sheet: -1.84 (0.60), residues: 82 loop : -1.26 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 54 HIS 0.001 0.000 HIS D 223 PHE 0.017 0.001 PHE A 53 TYR 0.004 0.001 TYR C 45 ARG 0.003 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.05 seconds wall clock time: 34 minutes 36.12 seconds (2076.12 seconds total)