Starting phenix.real_space_refine on Sat Apr 6 03:32:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shs_25135/04_2024/7shs_25135.pdb" } resolution = 4.1 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= 0.001 sd= 0.038 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 48 5.16 5 C 4545 2.51 5 N 1092 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6873 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2291 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "B" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2291 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2291 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Time building chain proxies: 4.26, per 1000 atoms: 0.62 Number of scatterers: 6873 At special positions: 0 Unit cell: (90.96, 81.864, 84.138, 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 48 16.00 O 1188 8.00 N 1092 7.00 C 4545 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 - 3.50 Amino acid : False - 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: 3.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.807A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.574A pdb=" N MET A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.843A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.743A pdb=" N CYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.845A pdb=" N LEU A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.587A pdb=" N ALA A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.807A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.574A pdb=" N MET B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 131 removed outlier: 3.844A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 159 removed outlier: 3.744A pdb=" N CYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.846A pdb=" N LEU B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.587A pdb=" N ALA B 248 " --> pdb=" O TRP B 244 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 95 removed outlier: 3.808A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.573A pdb=" N MET C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 removed outlier: 3.844A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 159 removed outlier: 3.744A pdb=" N CYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.845A pdb=" N LEU C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 269 removed outlier: 3.588A pdb=" N ALA C 248 " --> pdb=" O TRP C 244 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 447 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2076 1.35 - 1.46: 2092 1.46 - 1.58: 2864 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 7104 Sorted by residual: bond pdb=" CB MET C 82 " pdb=" CG MET C 82 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.93e-01 bond pdb=" CB MET A 82 " pdb=" CG MET A 82 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.90e-01 bond pdb=" CB MET B 82 " pdb=" CG MET B 82 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.49e-01 bond pdb=" C CYS B 120 " pdb=" N PRO B 121 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.28e-01 bond pdb=" CB MET C 186 " pdb=" CG MET C 186 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 7099 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.96: 165 106.96 - 113.78: 3645 113.78 - 120.60: 3205 120.60 - 127.42: 2549 127.42 - 134.24: 96 Bond angle restraints: 9660 Sorted by residual: angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" CB MET A 82 " pdb=" CG MET A 82 " pdb=" SD MET A 82 " ideal model delta sigma weight residual 112.70 121.80 -9.10 3.00e+00 1.11e-01 9.21e+00 angle pdb=" CB MET C 82 " pdb=" CG MET C 82 " pdb=" SD MET C 82 " ideal model delta sigma weight residual 112.70 121.79 -9.09 3.00e+00 1.11e-01 9.17e+00 angle pdb=" CB MET B 16 " pdb=" CG MET B 16 " pdb=" SD MET B 16 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" CB MET A 16 " pdb=" CG MET A 16 " pdb=" SD MET A 16 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.96e+00 ... (remaining 9655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3602 17.70 - 35.40: 301 35.40 - 53.11: 36 53.11 - 70.81: 6 70.81 - 88.51: 12 Dihedral angle restraints: 3957 sinusoidal: 1491 harmonic: 2466 Sorted by residual: dihedral pdb=" CA ASP B 272 " pdb=" C ASP B 272 " pdb=" N GLU B 273 " pdb=" CA GLU B 273 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ASP C 272 " pdb=" C ASP C 272 " pdb=" N GLU C 273 " pdb=" CA GLU C 273 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASP A 272 " pdb=" C ASP A 272 " pdb=" N GLU A 273 " pdb=" CA GLU A 273 " ideal model delta harmonic sigma weight residual -180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 624 0.029 - 0.058: 212 0.058 - 0.087: 129 0.087 - 0.116: 31 0.116 - 0.145: 9 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CA ASP A 253 " pdb=" N ASP A 253 " pdb=" C ASP A 253 " pdb=" CB ASP A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ASP B 253 " pdb=" N ASP B 253 " pdb=" C ASP B 253 " pdb=" CB ASP B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ASP C 253 " pdb=" N ASP C 253 " pdb=" C ASP C 253 " pdb=" CB ASP C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1002 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 223 " 0.014 2.00e-02 2.50e+03 1.49e-02 5.51e+00 pdb=" CG TRP C 223 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 223 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 223 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 223 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " 0.014 2.00e-02 2.50e+03 1.48e-02 5.50e+00 pdb=" CG TRP B 223 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 223 " -0.014 2.00e-02 2.50e+03 1.47e-02 5.39e+00 pdb=" CG TRP A 223 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 223 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 223 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 223 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 223 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 223 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 223 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 223 " 0.000 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2536 2.86 - 3.37: 7146 3.37 - 3.88: 11704 3.88 - 4.39: 12583 4.39 - 4.90: 21034 Nonbonded interactions: 55003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 69 " pdb=" N ARG B 136 " model vdw 2.349 2.520 nonbonded pdb=" O ASP A 242 " pdb=" OG1 THR A 245 " model vdw 2.354 2.440 nonbonded pdb=" O ASP C 242 " pdb=" OG1 THR C 245 " model vdw 2.354 2.440 nonbonded pdb=" O ASP B 242 " pdb=" OG1 THR B 245 " model vdw 2.355 2.440 nonbonded pdb=" OE1 GLN C 192 " pdb=" NH2 ARG C 195 " model vdw 2.388 2.520 ... (remaining 54998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.470 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: 0.000 Extract box with map and model: 2.610 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.250 Find NCS groups from input model: 0.420 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 0.030 7104 Z= 0.174 Angle : 0.740 9.123 9660 Z= 0.370 Chirality : 0.040 0.145 1005 Planarity : 0.005 0.050 1206 Dihedral : 13.648 88.509 2397 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.74 (0.27), residues: 843 helix: 0.85 (0.20), residues: 615 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 223 HIS 0.001 0.000 HIS C 210 PHE 0.014 0.001 PHE C 276 TYR 0.026 0.001 TYR A 156 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.813 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 10 MET cc_start: 0.8266 (pmm) cc_final: 0.7989 (ppp) REVERT: A 126 ASP cc_start: 0.8657 (t0) cc_final: 0.8269 (t0) REVERT: A 158 GLU cc_start: 0.8676 (tp30) cc_final: 0.8259 (tm-30) REVERT: A 177 TRP cc_start: 0.8306 (m100) cc_final: 0.8093 (m100) REVERT: A 250 CYS cc_start: 0.8771 (m) cc_final: 0.8270 (m) REVERT: B 34 TRP cc_start: 0.6187 (m-10) cc_final: 0.5752 (m100) REVERT: B 182 TYR cc_start: 0.6720 (t80) cc_final: 0.6194 (t80) REVERT: B 240 ILE cc_start: 0.7110 (pt) cc_final: 0.6806 (tp) REVERT: B 246 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7445 (pp20) REVERT: B 254 ILE cc_start: 0.8982 (mm) cc_final: 0.8611 (mm) REVERT: B 260 TYR cc_start: 0.7404 (t80) cc_final: 0.7027 (t80) REVERT: C 70 GLU cc_start: 0.8353 (pm20) cc_final: 0.7873 (pm20) REVERT: C 72 ASN cc_start: 0.8193 (m-40) cc_final: 0.7823 (m-40) REVERT: C 130 GLN cc_start: 0.8802 (mm110) cc_final: 0.8102 (mm110) REVERT: C 246 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 251 VAL cc_start: 0.9084 (m) cc_final: 0.8870 (t) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2442 time to fit residues: 69.4987 Evaluate side-chains 125 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 72 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7104 Z= 0.225 Angle : 0.597 6.868 9660 Z= 0.318 Chirality : 0.040 0.122 1005 Planarity : 0.005 0.049 1206 Dihedral : 4.170 19.963 942 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.87 % 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: 1.83 (0.29), residues: 843 helix: 1.59 (0.21), residues: 618 sheet: None (None), residues: 0 loop : 0.35 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 230 HIS 0.005 0.001 HIS C 249 PHE 0.023 0.002 PHE B 226 TYR 0.021 0.002 TYR C 111 ARG 0.004 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8385 (pmm) cc_final: 0.8134 (ppp) REVERT: A 92 ASP cc_start: 0.8835 (m-30) cc_final: 0.8633 (m-30) REVERT: A 126 ASP cc_start: 0.8744 (t0) cc_final: 0.8443 (t0) REVERT: A 131 LEU cc_start: 0.9336 (tp) cc_final: 0.9121 (tp) REVERT: A 250 CYS cc_start: 0.8609 (m) cc_final: 0.8283 (m) REVERT: B 10 MET cc_start: 0.8705 (mtm) cc_final: 0.8363 (mmt) REVERT: B 34 TRP cc_start: 0.6305 (m-10) cc_final: 0.5847 (m100) REVERT: B 40 LEU cc_start: 0.9106 (mp) cc_final: 0.8510 (tp) REVERT: B 82 MET cc_start: 0.8426 (ttp) cc_final: 0.8033 (ttp) REVERT: B 110 ASN cc_start: 0.8531 (p0) cc_final: 0.7731 (t0) REVERT: B 117 MET cc_start: 0.8644 (mmp) cc_final: 0.8366 (mmm) REVERT: B 123 LEU cc_start: 0.9343 (mt) cc_final: 0.9123 (mt) REVERT: B 210 HIS cc_start: 0.7562 (m90) cc_final: 0.7258 (m170) REVERT: B 246 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7580 (pp20) REVERT: B 260 TYR cc_start: 0.7677 (t80) cc_final: 0.6993 (t80) REVERT: C 67 TYR cc_start: 0.7631 (m-80) cc_final: 0.7404 (m-80) REVERT: C 70 GLU cc_start: 0.8435 (pm20) cc_final: 0.8233 (pm20) REVERT: C 72 ASN cc_start: 0.8285 (m-40) cc_final: 0.8085 (m-40) REVERT: C 88 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8197 (mtmm) REVERT: C 94 LEU cc_start: 0.7761 (mt) cc_final: 0.7469 (mm) REVERT: C 127 LEU cc_start: 0.8822 (pp) cc_final: 0.8578 (pp) REVERT: C 130 GLN cc_start: 0.8844 (mm110) cc_final: 0.8140 (mm110) REVERT: C 131 LEU cc_start: 0.9244 (tp) cc_final: 0.8898 (tp) REVERT: C 171 TYR cc_start: 0.7442 (t80) cc_final: 0.6759 (t80) REVERT: C 175 CYS cc_start: 0.8464 (m) cc_final: 0.8148 (p) REVERT: C 230 TRP cc_start: 0.8586 (t60) cc_final: 0.6915 (t60) REVERT: C 246 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1502 time to fit residues: 32.9598 Evaluate side-chains 114 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 9 GLN B 192 GLN C 3 HIS ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7104 Z= 0.201 Angle : 0.563 7.328 9660 Z= 0.295 Chirality : 0.039 0.116 1005 Planarity : 0.004 0.051 1206 Dihedral : 4.061 19.851 942 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.14 % Allowed : 3.70 % Favored : 96.15 % 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: 2.12 (0.29), residues: 843 helix: 1.84 (0.21), residues: 609 sheet: None (None), residues: 0 loop : 0.39 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 177 HIS 0.005 0.001 HIS C 249 PHE 0.016 0.002 PHE B 226 TYR 0.019 0.002 TYR C 46 ARG 0.003 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.8390 (pmm) cc_final: 0.8142 (ppp) REVERT: A 126 ASP cc_start: 0.8680 (t0) cc_final: 0.8391 (t0) REVERT: A 131 LEU cc_start: 0.9376 (tp) cc_final: 0.9094 (tp) REVERT: B 34 TRP cc_start: 0.6172 (m-10) cc_final: 0.5913 (m100) REVERT: B 40 LEU cc_start: 0.9182 (mp) cc_final: 0.8870 (tp) REVERT: B 82 MET cc_start: 0.8381 (ttp) cc_final: 0.8021 (ttm) REVERT: B 110 ASN cc_start: 0.8374 (p0) cc_final: 0.7629 (t0) REVERT: B 117 MET cc_start: 0.8618 (mmp) cc_final: 0.8286 (mmm) REVERT: B 123 LEU cc_start: 0.9351 (mt) cc_final: 0.8946 (tt) REVERT: B 210 HIS cc_start: 0.7557 (m90) cc_final: 0.7252 (m170) REVERT: B 257 LYS cc_start: 0.8037 (mptt) cc_final: 0.7730 (mmmm) REVERT: B 260 TYR cc_start: 0.7723 (t80) cc_final: 0.7292 (t80) REVERT: C 70 GLU cc_start: 0.8447 (pm20) cc_final: 0.8133 (pm20) REVERT: C 72 ASN cc_start: 0.8368 (m-40) cc_final: 0.8058 (m-40) REVERT: C 82 MET cc_start: 0.8480 (ttp) cc_final: 0.8048 (ttp) REVERT: C 88 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8220 (mtmm) REVERT: C 94 LEU cc_start: 0.7705 (mt) cc_final: 0.7094 (mm) REVERT: C 117 MET cc_start: 0.8440 (mmp) cc_final: 0.7493 (tpp) REVERT: C 127 LEU cc_start: 0.8842 (pp) cc_final: 0.8594 (pp) REVERT: C 130 GLN cc_start: 0.8786 (mm110) cc_final: 0.8108 (mm110) REVERT: C 171 TYR cc_start: 0.7883 (t80) cc_final: 0.6996 (t80) REVERT: C 219 PHE cc_start: 0.8198 (m-10) cc_final: 0.7930 (m-10) REVERT: C 223 TRP cc_start: 0.8282 (m-90) cc_final: 0.7580 (m-90) REVERT: C 230 TRP cc_start: 0.8689 (t60) cc_final: 0.7229 (t60) REVERT: C 260 TYR cc_start: 0.7392 (t80) cc_final: 0.7181 (t80) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1509 time to fit residues: 29.5514 Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 76 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7104 Z= 0.132 Angle : 0.513 7.553 9660 Z= 0.260 Chirality : 0.037 0.110 1005 Planarity : 0.003 0.048 1206 Dihedral : 3.822 17.917 942 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % 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: 2.42 (0.30), residues: 843 helix: 2.06 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.46 (0.46), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 177 HIS 0.011 0.001 HIS C 3 PHE 0.025 0.001 PHE B 217 TYR 0.014 0.001 TYR B 156 ARG 0.002 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8340 (pmm) cc_final: 0.8101 (ppp) REVERT: A 126 ASP cc_start: 0.8656 (t0) cc_final: 0.8349 (t0) REVERT: A 131 LEU cc_start: 0.9392 (tp) cc_final: 0.9082 (tp) REVERT: B 10 MET cc_start: 0.7448 (mmt) cc_final: 0.7148 (mmt) REVERT: B 34 TRP cc_start: 0.6054 (m-10) cc_final: 0.5710 (m100) REVERT: B 40 LEU cc_start: 0.9164 (mp) cc_final: 0.8768 (tp) REVERT: B 82 MET cc_start: 0.8360 (ttp) cc_final: 0.8061 (ttm) REVERT: B 110 ASN cc_start: 0.8315 (p0) cc_final: 0.7609 (t0) REVERT: B 117 MET cc_start: 0.8507 (mmp) cc_final: 0.8263 (mmm) REVERT: B 123 LEU cc_start: 0.9387 (mt) cc_final: 0.9015 (tt) REVERT: B 210 HIS cc_start: 0.7444 (m90) cc_final: 0.7151 (m170) REVERT: C 70 GLU cc_start: 0.8415 (pm20) cc_final: 0.8146 (pm20) REVERT: C 82 MET cc_start: 0.8397 (ttp) cc_final: 0.8121 (ttp) REVERT: C 88 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8223 (mtmm) REVERT: C 94 LEU cc_start: 0.7632 (mt) cc_final: 0.7147 (mt) REVERT: C 117 MET cc_start: 0.8219 (mmp) cc_final: 0.6486 (tmm) REVERT: C 125 TYR cc_start: 0.8032 (t80) cc_final: 0.7714 (t80) REVERT: C 130 GLN cc_start: 0.8711 (mm110) cc_final: 0.7967 (mm110) REVERT: C 171 TYR cc_start: 0.8052 (t80) cc_final: 0.7363 (t80) REVERT: C 230 TRP cc_start: 0.8743 (t60) cc_final: 0.7156 (t60) REVERT: C 246 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8063 (mm-30) REVERT: C 260 TYR cc_start: 0.7393 (t80) cc_final: 0.7167 (t80) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1600 time to fit residues: 30.3370 Evaluate side-chains 108 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7104 Z= 0.204 Angle : 0.558 7.602 9660 Z= 0.297 Chirality : 0.040 0.118 1005 Planarity : 0.004 0.048 1206 Dihedral : 4.046 19.209 942 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.14 % Allowed : 2.42 % Favored : 97.44 % 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: 2.23 (0.30), residues: 843 helix: 1.92 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.41 (0.47), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 34 HIS 0.006 0.001 HIS C 210 PHE 0.014 0.002 PHE B 76 TYR 0.024 0.002 TYR B 156 ARG 0.003 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8356 (pmm) cc_final: 0.8102 (ppp) REVERT: A 126 ASP cc_start: 0.8635 (t0) cc_final: 0.8390 (t0) REVERT: A 131 LEU cc_start: 0.9389 (tp) cc_final: 0.9063 (tp) REVERT: A 176 PHE cc_start: 0.8604 (t80) cc_final: 0.8372 (t80) REVERT: A 257 LYS cc_start: 0.9165 (mptt) cc_final: 0.8898 (mmtm) REVERT: B 10 MET cc_start: 0.7226 (mmt) cc_final: 0.6906 (mmt) REVERT: B 40 LEU cc_start: 0.9044 (mp) cc_final: 0.8796 (mm) REVERT: B 82 MET cc_start: 0.8408 (ttp) cc_final: 0.8183 (ttp) REVERT: B 108 PHE cc_start: 0.7879 (t80) cc_final: 0.7644 (t80) REVERT: B 110 ASN cc_start: 0.8186 (p0) cc_final: 0.7834 (t0) REVERT: B 117 MET cc_start: 0.8604 (mmp) cc_final: 0.8217 (mmm) REVERT: B 260 TYR cc_start: 0.7443 (t80) cc_final: 0.7006 (t80) REVERT: C 16 MET cc_start: 0.8412 (mmp) cc_final: 0.7591 (tpp) REVERT: C 70 GLU cc_start: 0.8530 (pm20) cc_final: 0.8327 (pm20) REVERT: C 82 MET cc_start: 0.8403 (ttp) cc_final: 0.8199 (ttp) REVERT: C 88 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8115 (mtmm) REVERT: C 94 LEU cc_start: 0.7712 (mt) cc_final: 0.7017 (mt) REVERT: C 108 PHE cc_start: 0.7438 (t80) cc_final: 0.7220 (t80) REVERT: C 130 GLN cc_start: 0.8720 (mm110) cc_final: 0.8080 (mm110) REVERT: C 131 LEU cc_start: 0.9347 (tp) cc_final: 0.9045 (tp) REVERT: C 171 TYR cc_start: 0.8356 (t80) cc_final: 0.8094 (t80) REVERT: C 246 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8049 (mm-30) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1491 time to fit residues: 27.9260 Evaluate side-chains 105 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7104 Z= 0.148 Angle : 0.520 7.677 9660 Z= 0.266 Chirality : 0.038 0.117 1005 Planarity : 0.003 0.040 1206 Dihedral : 3.853 19.164 942 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 2.39 (0.30), residues: 843 helix: 2.02 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.53 (0.47), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 223 HIS 0.007 0.001 HIS C 210 PHE 0.011 0.001 PHE B 173 TYR 0.017 0.001 TYR A 156 ARG 0.002 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8334 (pmm) cc_final: 0.8102 (ppp) REVERT: A 126 ASP cc_start: 0.8650 (t0) cc_final: 0.8327 (t0) REVERT: A 131 LEU cc_start: 0.9402 (tp) cc_final: 0.9054 (tp) REVERT: A 257 LYS cc_start: 0.9159 (mptt) cc_final: 0.8890 (mmtm) REVERT: B 40 LEU cc_start: 0.9173 (mp) cc_final: 0.8823 (mp) REVERT: B 82 MET cc_start: 0.8316 (ttp) cc_final: 0.8082 (ttp) REVERT: B 108 PHE cc_start: 0.7937 (t80) cc_final: 0.7564 (t80) REVERT: B 110 ASN cc_start: 0.8128 (p0) cc_final: 0.7694 (t0) REVERT: B 117 MET cc_start: 0.8521 (mmp) cc_final: 0.8203 (mmm) REVERT: B 260 TYR cc_start: 0.7218 (t80) cc_final: 0.6930 (t80) REVERT: C 16 MET cc_start: 0.8392 (mmp) cc_final: 0.7571 (tpp) REVERT: C 70 GLU cc_start: 0.8492 (pm20) cc_final: 0.8263 (pm20) REVERT: C 82 MET cc_start: 0.8424 (ttp) cc_final: 0.8186 (ttp) REVERT: C 94 LEU cc_start: 0.7587 (mt) cc_final: 0.7023 (mm) REVERT: C 108 PHE cc_start: 0.7239 (t80) cc_final: 0.6988 (t80) REVERT: C 117 MET cc_start: 0.8263 (mmp) cc_final: 0.6478 (tmm) REVERT: C 130 GLN cc_start: 0.8670 (mm110) cc_final: 0.7836 (mm110) REVERT: C 131 LEU cc_start: 0.9345 (tp) cc_final: 0.8980 (tp) REVERT: C 148 MET cc_start: 0.8811 (ttp) cc_final: 0.8119 (tmm) REVERT: C 171 TYR cc_start: 0.8425 (t80) cc_final: 0.8181 (t80) REVERT: C 246 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8111 (mm-30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1598 time to fit residues: 31.5325 Evaluate side-chains 108 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 9 GLN B 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7104 Z= 0.138 Angle : 0.521 7.928 9660 Z= 0.265 Chirality : 0.038 0.137 1005 Planarity : 0.003 0.045 1206 Dihedral : 3.756 17.655 942 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.14 % Allowed : 1.28 % Favored : 98.58 % 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: 2.74 (0.30), residues: 843 helix: 2.29 (0.21), residues: 591 sheet: None (None), residues: 0 loop : 0.77 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 230 HIS 0.008 0.001 HIS C 210 PHE 0.014 0.001 PHE C 104 TYR 0.019 0.001 TYR A 156 ARG 0.002 0.000 ARG C 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8323 (pmm) cc_final: 0.8097 (ppp) REVERT: A 55 ARG cc_start: 0.5893 (mmt180) cc_final: 0.5332 (tpp-160) REVERT: A 126 ASP cc_start: 0.8632 (t0) cc_final: 0.8283 (t0) REVERT: A 131 LEU cc_start: 0.9409 (tp) cc_final: 0.9079 (tp) REVERT: A 257 LYS cc_start: 0.9153 (mptt) cc_final: 0.8892 (mmtm) REVERT: B 40 LEU cc_start: 0.9166 (mp) cc_final: 0.8832 (mm) REVERT: B 82 MET cc_start: 0.8380 (ttp) cc_final: 0.8004 (ttp) REVERT: B 108 PHE cc_start: 0.8064 (t80) cc_final: 0.7702 (t80) REVERT: B 110 ASN cc_start: 0.8100 (p0) cc_final: 0.7635 (t0) REVERT: B 117 MET cc_start: 0.8534 (mmp) cc_final: 0.8220 (mmm) REVERT: B 171 TYR cc_start: 0.7769 (t80) cc_final: 0.7543 (t80) REVERT: B 260 TYR cc_start: 0.7065 (t80) cc_final: 0.6811 (t80) REVERT: C 16 MET cc_start: 0.8353 (mmp) cc_final: 0.7513 (tpp) REVERT: C 70 GLU cc_start: 0.8388 (pm20) cc_final: 0.8081 (pm20) REVERT: C 88 LYS cc_start: 0.8872 (mttt) cc_final: 0.8426 (mtmm) REVERT: C 94 LEU cc_start: 0.7621 (mt) cc_final: 0.6979 (mt) REVERT: C 108 PHE cc_start: 0.7223 (t80) cc_final: 0.6987 (t80) REVERT: C 123 LEU cc_start: 0.9237 (tt) cc_final: 0.8893 (tt) REVERT: C 127 LEU cc_start: 0.9177 (tt) cc_final: 0.8752 (mt) REVERT: C 130 GLN cc_start: 0.8660 (mm110) cc_final: 0.7922 (mm110) REVERT: C 171 TYR cc_start: 0.8596 (t80) cc_final: 0.8335 (t80) REVERT: C 235 ARG cc_start: 0.7439 (mmp80) cc_final: 0.6939 (mmp80) REVERT: C 246 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8098 (mm-30) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1672 time to fit residues: 31.8068 Evaluate side-chains 112 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 78 ASN B 9 GLN B 210 HIS C 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7104 Z= 0.132 Angle : 0.512 8.289 9660 Z= 0.260 Chirality : 0.037 0.128 1005 Planarity : 0.003 0.045 1206 Dihedral : 3.657 16.449 942 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.14 % Allowed : 0.71 % Favored : 99.15 % 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: 2.50 (0.30), residues: 843 helix: 2.11 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.53 (0.46), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 223 HIS 0.008 0.001 HIS C 210 PHE 0.016 0.001 PHE C 276 TYR 0.021 0.001 TYR A 156 ARG 0.001 0.000 ARG C 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8335 (pmm) cc_final: 0.8103 (ppp) REVERT: A 55 ARG cc_start: 0.6060 (mmt180) cc_final: 0.5569 (tpp-160) REVERT: A 126 ASP cc_start: 0.8608 (t0) cc_final: 0.8272 (t0) REVERT: A 131 LEU cc_start: 0.9428 (tp) cc_final: 0.9112 (tp) REVERT: A 257 LYS cc_start: 0.9192 (mptt) cc_final: 0.8973 (mmtm) REVERT: B 82 MET cc_start: 0.8402 (ttp) cc_final: 0.8003 (ttp) REVERT: B 108 PHE cc_start: 0.8077 (t80) cc_final: 0.7704 (t80) REVERT: B 110 ASN cc_start: 0.8040 (p0) cc_final: 0.7620 (t0) REVERT: B 117 MET cc_start: 0.8467 (mmp) cc_final: 0.8242 (mmm) REVERT: B 171 TYR cc_start: 0.7844 (t80) cc_final: 0.7569 (t80) REVERT: C 70 GLU cc_start: 0.8434 (pm20) cc_final: 0.8127 (pm20) REVERT: C 82 MET cc_start: 0.8445 (ttp) cc_final: 0.8147 (ttp) REVERT: C 88 LYS cc_start: 0.8854 (mttt) cc_final: 0.8516 (mttp) REVERT: C 94 LEU cc_start: 0.7632 (mt) cc_final: 0.6994 (mt) REVERT: C 117 MET cc_start: 0.8175 (mmp) cc_final: 0.7074 (tpp) REVERT: C 130 GLN cc_start: 0.8644 (mm110) cc_final: 0.7924 (mm110) REVERT: C 171 TYR cc_start: 0.8582 (t80) cc_final: 0.8340 (t80) REVERT: C 246 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8122 (mm-30) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1530 time to fit residues: 28.5013 Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7104 Z= 0.149 Angle : 0.525 8.550 9660 Z= 0.270 Chirality : 0.038 0.122 1005 Planarity : 0.003 0.046 1206 Dihedral : 3.695 15.316 942 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.29 % 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: 2.46 (0.30), residues: 843 helix: 2.08 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.53 (0.46), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 34 HIS 0.008 0.001 HIS C 210 PHE 0.015 0.001 PHE B 219 TYR 0.021 0.001 TYR A 156 ARG 0.004 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8327 (pmm) cc_final: 0.8125 (ppp) REVERT: A 55 ARG cc_start: 0.5989 (mmt180) cc_final: 0.5749 (tpp-160) REVERT: A 126 ASP cc_start: 0.8590 (t0) cc_final: 0.8273 (t0) REVERT: A 131 LEU cc_start: 0.9422 (tp) cc_final: 0.9090 (tp) REVERT: A 257 LYS cc_start: 0.9186 (mptt) cc_final: 0.8933 (mmtm) REVERT: B 40 LEU cc_start: 0.9150 (mm) cc_final: 0.8875 (mm) REVERT: B 82 MET cc_start: 0.8370 (ttp) cc_final: 0.8025 (ttp) REVERT: B 108 PHE cc_start: 0.8167 (t80) cc_final: 0.7720 (t80) REVERT: B 110 ASN cc_start: 0.7992 (p0) cc_final: 0.7606 (t0) REVERT: B 117 MET cc_start: 0.8543 (mmp) cc_final: 0.8228 (mmm) REVERT: C 70 GLU cc_start: 0.8474 (pm20) cc_final: 0.8130 (pm20) REVERT: C 82 MET cc_start: 0.8392 (ttp) cc_final: 0.8056 (ttp) REVERT: C 88 LYS cc_start: 0.8848 (mttt) cc_final: 0.8550 (mttp) REVERT: C 94 LEU cc_start: 0.7620 (mt) cc_final: 0.6934 (mt) REVERT: C 117 MET cc_start: 0.8205 (mmp) cc_final: 0.7115 (tpp) REVERT: C 130 GLN cc_start: 0.8644 (mm110) cc_final: 0.7811 (mm110) REVERT: C 171 TYR cc_start: 0.8640 (t80) cc_final: 0.8362 (t80) REVERT: C 246 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8146 (mm-30) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1546 time to fit residues: 28.7596 Evaluate side-chains 104 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7104 Z= 0.252 Angle : 0.631 9.019 9660 Z= 0.337 Chirality : 0.042 0.143 1005 Planarity : 0.004 0.046 1206 Dihedral : 4.238 18.036 942 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.29), residues: 843 helix: 1.63 (0.20), residues: 612 sheet: None (None), residues: 0 loop : 0.26 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 34 HIS 0.008 0.002 HIS C 249 PHE 0.022 0.002 PHE A 276 TYR 0.024 0.002 TYR C 46 ARG 0.004 0.001 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8359 (pmm) cc_final: 0.8145 (ppp) REVERT: A 126 ASP cc_start: 0.8600 (t0) cc_final: 0.8353 (t0) REVERT: A 131 LEU cc_start: 0.9401 (tp) cc_final: 0.9089 (tp) REVERT: A 176 PHE cc_start: 0.8503 (t80) cc_final: 0.8283 (t80) REVERT: B 82 MET cc_start: 0.8430 (ttp) cc_final: 0.8101 (ttp) REVERT: B 108 PHE cc_start: 0.8314 (t80) cc_final: 0.7780 (t80) REVERT: B 110 ASN cc_start: 0.7968 (p0) cc_final: 0.7684 (t0) REVERT: B 117 MET cc_start: 0.8567 (mmp) cc_final: 0.8194 (mmm) REVERT: C 70 GLU cc_start: 0.8613 (pm20) cc_final: 0.8363 (pm20) REVERT: C 88 LYS cc_start: 0.8863 (mttt) cc_final: 0.8650 (mttp) REVERT: C 94 LEU cc_start: 0.7737 (mt) cc_final: 0.7408 (mt) REVERT: C 117 MET cc_start: 0.8298 (mmp) cc_final: 0.7250 (tpp) REVERT: C 130 GLN cc_start: 0.8722 (mm110) cc_final: 0.7985 (mm110) REVERT: C 171 TYR cc_start: 0.8828 (t80) cc_final: 0.8509 (t80) REVERT: C 250 CYS cc_start: 0.8857 (m) cc_final: 0.8312 (t) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1564 time to fit residues: 26.4473 Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0270 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 9 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065963 restraints weight = 34403.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067678 restraints weight = 19781.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068881 restraints weight = 13043.995| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7104 Z= 0.137 Angle : 0.545 8.359 9660 Z= 0.276 Chirality : 0.038 0.142 1005 Planarity : 0.003 0.044 1206 Dihedral : 3.823 16.139 942 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.29 % 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: 2.39 (0.29), residues: 843 helix: 2.06 (0.21), residues: 591 sheet: None (None), residues: 0 loop : 0.57 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.005 0.001 HIS A 33 PHE 0.018 0.001 PHE A 276 TYR 0.015 0.001 TYR C 46 ARG 0.002 0.000 ARG C 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.77 seconds wall clock time: 28 minutes 5.90 seconds (1685.90 seconds total)