Starting phenix.real_space_refine on Thu Nov 14 12:32:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sv1_40781/11_2024/8sv1_40781.cif" } resolution = 3.5 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= 0.068 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 54 5.16 5 C 4004 2.51 5 N 1062 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1158 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 718 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "a" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1158 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "b" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 718 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "C" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1289 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1289 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.51, per 1000 atoms: 0.71 Number of scatterers: 6330 At special positions: 0 Unit cell: (72.21, 135.29, 65.57, 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 54 16.00 O 1210 8.00 N 1062 7.00 C 4004 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: 1.44 Conformation dependent library (CDL) restraints added in 961.0 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 19.7% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.517A pdb=" N LEU A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.751A pdb=" N LYS A 274 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 361 Processing helix chain 'B' and resid 365 through 376 Processing helix chain 'a' and resid 181 through 197 Processing helix chain 'a' and resid 207 through 221 Processing helix chain 'a' and resid 223 through 227 Processing helix chain 'a' and resid 257 through 264 Processing helix chain 'a' and resid 270 through 274 removed outlier: 3.558A pdb=" N LYS a 274 " --> pdb=" O PRO a 271 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 361 removed outlier: 3.573A pdb=" N ALA b 361 " --> pdb=" O MET b 357 " (cutoff:3.500A) Processing helix chain 'b' and resid 365 through 376 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.554A pdb=" N LEU A 232 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 278 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 removed outlier: 3.863A pdb=" N PHE A 295 " --> pdb=" O LYS b 319 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS b 319 " --> pdb=" O PHE A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AA5, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AA6, first strand: chain 'a' and resid 199 through 204 removed outlier: 3.516A pdb=" N ALA a 165 " --> pdb=" O SER a 199 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE a 231 " --> pdb=" O LEU a 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU a 232 " --> pdb=" O VAL a 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 243 through 244 Processing sheet with id=AA8, first strand: chain 'b' and resid 340 through 341 Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.721A pdb=" N ALA C 162 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 161 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 187 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 18.414A pdb=" N ILE C 185 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 13.593A pdb=" N SER C 153 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 187 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 151 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 189 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 149 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 97 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 46 removed outlier: 5.857A pdb=" N SER C 46 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN C 190 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 18.414A pdb=" N ILE C 185 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 13.593A pdb=" N SER C 153 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 187 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 151 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 189 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 149 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 100 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 110 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 24 through 25 removed outlier: 3.721A pdb=" N ALA c 162 " --> pdb=" O ILE c 173 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU c 161 " --> pdb=" O PHE c 187 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE c 187 " --> pdb=" O LEU c 161 " (cutoff:3.500A) removed outlier: 18.414A pdb=" N ILE c 185 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 13.592A pdb=" N SER c 153 " --> pdb=" O ILE c 185 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE c 187 " --> pdb=" O PHE c 151 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE c 151 " --> pdb=" O PHE c 187 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL c 189 " --> pdb=" O MET c 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET c 149 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA c 97 " --> pdb=" O TYR c 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 45 through 46 removed outlier: 5.856A pdb=" N SER c 46 " --> pdb=" O THR c 188 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN c 190 " --> pdb=" O SER c 46 " (cutoff:3.500A) removed outlier: 18.414A pdb=" N ILE c 185 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 13.592A pdb=" N SER c 153 " --> pdb=" O ILE c 185 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE c 187 " --> pdb=" O PHE c 151 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE c 151 " --> pdb=" O PHE c 187 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL c 189 " --> pdb=" O MET c 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET c 149 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE c 100 " --> pdb=" O LEU c 110 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU c 110 " --> pdb=" O ILE c 100 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 519 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: 1.94 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1983 1.33 - 1.46: 1005 1.46 - 1.58: 3378 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 6450 Sorted by residual: bond pdb=" N PHE C 83 " pdb=" CA PHE C 83 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.84e+00 bond pdb=" N PHE c 83 " pdb=" CA PHE c 83 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.62e+00 bond pdb=" N MET C 122 " pdb=" CA MET C 122 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.89e+00 bond pdb=" N MET c 122 " pdb=" CA MET c 122 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.42e+00 bond pdb=" C ARG a 221 " pdb=" N PRO a 222 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.67e+00 ... (remaining 6445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 8629 3.47 - 6.94: 44 6.94 - 10.42: 7 10.42 - 13.89: 0 13.89 - 17.36: 2 Bond angle restraints: 8682 Sorted by residual: angle pdb=" N ILE c 84 " pdb=" CA ILE c 84 " pdb=" C ILE c 84 " ideal model delta sigma weight residual 109.30 125.39 -16.09 1.25e+00 6.40e-01 1.66e+02 angle pdb=" N ILE C 84 " pdb=" CA ILE C 84 " pdb=" C ILE C 84 " ideal model delta sigma weight residual 109.37 126.73 -17.36 1.35e+00 5.49e-01 1.65e+02 angle pdb=" N ILE c 84 " pdb=" CA ILE c 84 " pdb=" CB ILE c 84 " ideal model delta sigma weight residual 110.31 101.58 8.73 1.23e+00 6.61e-01 5.04e+01 angle pdb=" N ILE C 84 " pdb=" CA ILE C 84 " pdb=" CB ILE C 84 " ideal model delta sigma weight residual 110.13 101.48 8.65 1.34e+00 5.57e-01 4.17e+01 angle pdb=" CA ARG b 383 " pdb=" C ARG b 383 " pdb=" O ARG b 383 " ideal model delta sigma weight residual 122.36 118.10 4.26 1.21e+00 6.83e-01 1.24e+01 ... (remaining 8677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 3240 14.05 - 28.10: 475 28.10 - 42.14: 187 42.14 - 56.19: 37 56.19 - 70.24: 15 Dihedral angle restraints: 3954 sinusoidal: 1636 harmonic: 2318 Sorted by residual: dihedral pdb=" CA VAL C 47 " pdb=" C VAL C 47 " pdb=" N ILE C 48 " pdb=" CA ILE C 48 " ideal model delta harmonic sigma weight residual 180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA VAL c 47 " pdb=" C VAL c 47 " pdb=" N ILE c 48 " pdb=" CA ILE c 48 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU C 105 " pdb=" C GLU C 105 " pdb=" N LYS C 106 " pdb=" CA LYS C 106 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 781 0.058 - 0.116: 164 0.116 - 0.175: 17 0.175 - 0.233: 1 0.233 - 0.291: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE c 84 " pdb=" N ILE c 84 " pdb=" C ILE c 84 " pdb=" CB ILE c 84 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 318 " pdb=" CA ILE B 318 " pdb=" CG1 ILE B 318 " pdb=" CG2 ILE B 318 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 961 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG c 49 " 0.474 9.50e-02 1.11e+02 2.13e-01 2.76e+01 pdb=" NE ARG c 49 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG c 49 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG c 49 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG c 49 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 49 " -0.474 9.50e-02 1.11e+02 2.13e-01 2.76e+01 pdb=" NE ARG C 49 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 49 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 49 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 49 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 383 " 0.415 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG b 383 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG b 383 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG b 383 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG b 383 " 0.014 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 883 2.76 - 3.29: 6106 3.29 - 3.83: 10062 3.83 - 4.36: 11584 4.36 - 4.90: 20099 Nonbonded interactions: 48734 Sorted by model distance: nonbonded pdb=" OG1 THR A 162 " pdb=" OG1 THR A 226 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 332 " pdb=" OG SER B 339 " model vdw 2.226 3.040 nonbonded pdb=" O THR a 162 " pdb=" OG1 THR a 162 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 198 " pdb=" OG SER A 229 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU b 324 " pdb=" NH2 ARG b 391 " model vdw 2.300 3.120 ... (remaining 48729 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' 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: 0.900 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.600 Find NCS groups from input model: 0.180 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 0.036 6450 Z= 0.221 Angle : 0.755 17.360 8682 Z= 0.439 Chirality : 0.046 0.291 964 Planarity : 0.012 0.213 1122 Dihedral : 16.023 70.239 2438 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.19 % Favored : 93.43 % Rotamer: Outliers : 0.70 % Allowed : 17.69 % Favored : 81.62 % 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: -1.32 (0.29), residues: 776 helix: 1.09 (0.43), residues: 136 sheet: -0.71 (0.44), residues: 158 loop : -1.59 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP b 340 HIS 0.005 0.001 HIS a 224 PHE 0.010 0.001 PHE C 18 TYR 0.007 0.001 TYR c 88 ARG 0.005 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 258 time to evaluate : 0.758 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 161 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6776 (ptt180) REVERT: A 283 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6709 (tm-30) REVERT: a 225 LYS cc_start: 0.8484 (tttt) cc_final: 0.8251 (mmtp) REVERT: a 272 SER cc_start: 0.7953 (m) cc_final: 0.7554 (m) REVERT: a 283 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6670 (tm-30) REVERT: a 296 LYS cc_start: 0.8569 (tppt) cc_final: 0.7754 (mtpt) REVERT: C 50 ASN cc_start: 0.7295 (m110) cc_final: 0.7031 (m110) REVERT: C 164 GLU cc_start: 0.5615 (tp30) cc_final: 0.5142 (tp30) REVERT: c 50 ASN cc_start: 0.7226 (m110) cc_final: 0.6936 (m110) REVERT: c 164 GLU cc_start: 0.5408 (tp30) cc_final: 0.5030 (tp30) outliers start: 5 outliers final: 3 residues processed: 259 average time/residue: 0.2149 time to fit residues: 70.5901 Evaluate side-chains 233 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 230 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 383 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain c residue 49 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 337 ASN C 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6450 Z= 0.228 Angle : 0.638 8.038 8682 Z= 0.334 Chirality : 0.046 0.175 964 Planarity : 0.005 0.056 1122 Dihedral : 6.266 59.503 852 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.92 % Allowed : 21.73 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.29), residues: 776 helix: 0.99 (0.43), residues: 138 sheet: -0.56 (0.45), residues: 148 loop : -1.64 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 294 HIS 0.005 0.001 HIS A 224 PHE 0.027 0.002 PHE b 370 TYR 0.007 0.001 TYR c 88 ARG 0.004 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLN cc_start: 0.7755 (mp10) cc_final: 0.7523 (mp10) REVERT: A 283 GLN cc_start: 0.7538 (tm-30) cc_final: 0.6736 (tm-30) REVERT: a 225 LYS cc_start: 0.8603 (tttt) cc_final: 0.8386 (mmtp) REVERT: a 241 GLU cc_start: 0.8173 (mp0) cc_final: 0.7956 (mp0) REVERT: a 283 GLN cc_start: 0.7431 (tm-30) cc_final: 0.6578 (tm-30) REVERT: a 296 LYS cc_start: 0.8504 (tppt) cc_final: 0.7742 (mttt) REVERT: C 50 ASN cc_start: 0.7132 (m110) cc_final: 0.6847 (m110) REVERT: C 164 GLU cc_start: 0.5352 (tp30) cc_final: 0.5081 (tp30) REVERT: c 50 ASN cc_start: 0.6803 (m110) cc_final: 0.6500 (m110) REVERT: c 176 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8173 (mtmt) outliers start: 21 outliers final: 16 residues processed: 227 average time/residue: 0.2173 time to fit residues: 62.3827 Evaluate side-chains 227 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 383 ARG Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 chunk 74 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6450 Z= 0.225 Angle : 0.610 7.758 8682 Z= 0.315 Chirality : 0.045 0.266 964 Planarity : 0.005 0.055 1122 Dihedral : 6.219 59.153 852 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.04 % Allowed : 20.75 % Favored : 75.21 % 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: -1.36 (0.29), residues: 776 helix: 0.99 (0.43), residues: 138 sheet: -0.70 (0.44), residues: 148 loop : -1.61 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 340 HIS 0.004 0.001 HIS B 322 PHE 0.013 0.001 PHE b 327 TYR 0.013 0.001 TYR C 37 ARG 0.005 0.000 ARG b 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.739 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 214 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8081 (tp30) REVERT: A 283 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6721 (tm-30) REVERT: a 225 LYS cc_start: 0.8624 (tttt) cc_final: 0.8363 (mttm) REVERT: a 241 GLU cc_start: 0.8170 (mp0) cc_final: 0.7915 (mp0) REVERT: a 283 GLN cc_start: 0.7347 (tm-30) cc_final: 0.6447 (tm-30) REVERT: a 296 LYS cc_start: 0.8471 (tppt) cc_final: 0.7720 (mttt) REVERT: C 50 ASN cc_start: 0.7084 (m110) cc_final: 0.6813 (m110) REVERT: c 164 GLU cc_start: 0.6051 (tp30) cc_final: 0.5833 (tp30) outliers start: 29 outliers final: 22 residues processed: 236 average time/residue: 0.2073 time to fit residues: 62.4887 Evaluate side-chains 234 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 0.0070 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN b 385 GLN C 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6450 Z= 0.158 Angle : 0.586 8.130 8682 Z= 0.300 Chirality : 0.045 0.245 964 Planarity : 0.004 0.055 1122 Dihedral : 5.795 58.993 848 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.34 % Allowed : 24.09 % Favored : 72.56 % 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: -1.23 (0.29), residues: 776 helix: 1.08 (0.43), residues: 138 sheet: -0.59 (0.45), residues: 140 loop : -1.51 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 340 HIS 0.002 0.001 HIS B 322 PHE 0.026 0.001 PHE b 370 TYR 0.012 0.001 TYR C 37 ARG 0.004 0.000 ARG a 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7513 (tm-30) cc_final: 0.6776 (tm-30) REVERT: a 225 LYS cc_start: 0.8620 (tttt) cc_final: 0.8364 (mttm) REVERT: a 241 GLU cc_start: 0.8120 (mp0) cc_final: 0.7914 (mp0) REVERT: a 283 GLN cc_start: 0.7367 (tm-30) cc_final: 0.6584 (tm-30) REVERT: C 34 GLU cc_start: 0.6988 (mp0) cc_final: 0.6608 (mp0) REVERT: C 50 ASN cc_start: 0.7071 (m110) cc_final: 0.6796 (m110) REVERT: c 164 GLU cc_start: 0.6472 (tp30) cc_final: 0.6027 (tp30) REVERT: c 176 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7349 (mttt) outliers start: 24 outliers final: 21 residues processed: 226 average time/residue: 0.2059 time to fit residues: 59.2641 Evaluate side-chains 232 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN b 385 GLN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6450 Z= 0.427 Angle : 0.714 7.101 8682 Z= 0.375 Chirality : 0.048 0.259 964 Planarity : 0.005 0.057 1122 Dihedral : 6.384 57.240 848 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.74 % Allowed : 23.96 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.28), residues: 776 helix: 0.80 (0.43), residues: 138 sheet: -1.07 (0.43), residues: 140 loop : -1.77 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 294 HIS 0.006 0.002 HIS B 322 PHE 0.026 0.002 PHE b 370 TYR 0.014 0.002 TYR a 153 ARG 0.006 0.001 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7345 (tt0) cc_final: 0.6917 (tt0) REVERT: A 214 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8131 (tp30) REVERT: A 283 GLN cc_start: 0.7629 (tm-30) cc_final: 0.6799 (tm-30) REVERT: B 370 PHE cc_start: 0.7618 (m-10) cc_final: 0.7122 (m-10) REVERT: B 374 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6665 (mtm110) REVERT: a 225 LYS cc_start: 0.8712 (tttt) cc_final: 0.8378 (mmtp) REVERT: a 283 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7002 (tm-30) REVERT: a 296 LYS cc_start: 0.8423 (tppt) cc_final: 0.7660 (mttt) REVERT: C 34 GLU cc_start: 0.7149 (mp0) cc_final: 0.6946 (mp0) REVERT: C 50 ASN cc_start: 0.6896 (m110) cc_final: 0.6647 (m110) REVERT: C 140 ARG cc_start: 0.7941 (mpt90) cc_final: 0.7417 (mpt90) REVERT: c 164 GLU cc_start: 0.6507 (tp30) cc_final: 0.6151 (tp30) REVERT: c 176 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7302 (mttt) outliers start: 34 outliers final: 23 residues processed: 241 average time/residue: 0.2024 time to fit residues: 62.3947 Evaluate side-chains 241 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 205 ASN Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6450 Z= 0.283 Angle : 0.677 9.404 8682 Z= 0.344 Chirality : 0.046 0.257 964 Planarity : 0.005 0.056 1122 Dihedral : 5.584 54.932 844 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.01 % Allowed : 25.07 % Favored : 69.92 % 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: -1.65 (0.28), residues: 776 helix: 0.73 (0.42), residues: 138 sheet: -1.14 (0.44), residues: 140 loop : -1.69 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 294 HIS 0.013 0.002 HIS b 322 PHE 0.020 0.002 PHE b 327 TYR 0.010 0.001 TYR C 37 ARG 0.003 0.000 ARG a 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7249 (tt0) cc_final: 0.6857 (tt0) REVERT: A 214 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8119 (tp30) REVERT: A 283 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6649 (tm-30) REVERT: a 225 LYS cc_start: 0.8666 (tttt) cc_final: 0.8308 (mmtp) REVERT: a 283 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6522 (tm-30) REVERT: a 296 LYS cc_start: 0.8423 (tppt) cc_final: 0.7703 (mttm) REVERT: C 34 GLU cc_start: 0.7161 (mp0) cc_final: 0.6329 (mp0) REVERT: C 50 ASN cc_start: 0.6904 (m110) cc_final: 0.6647 (m110) REVERT: c 122 MET cc_start: 0.5865 (ptt) cc_final: 0.5561 (ppp) REVERT: c 164 GLU cc_start: 0.6605 (tp30) cc_final: 0.6193 (tp30) REVERT: c 174 LEU cc_start: 0.8616 (tt) cc_final: 0.8016 (tt) REVERT: c 176 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7152 (mttt) outliers start: 36 outliers final: 28 residues processed: 244 average time/residue: 0.2042 time to fit residues: 63.7777 Evaluate side-chains 250 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 205 ASN Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 366 VAL Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 61 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6450 Z= 0.224 Angle : 0.676 9.181 8682 Z= 0.341 Chirality : 0.046 0.232 964 Planarity : 0.004 0.056 1122 Dihedral : 5.494 57.902 844 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.87 % Allowed : 25.49 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 776 helix: 0.77 (0.41), residues: 138 sheet: -1.26 (0.43), residues: 140 loop : -1.61 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 294 HIS 0.009 0.001 HIS b 322 PHE 0.016 0.002 PHE b 327 TYR 0.012 0.001 TYR C 37 ARG 0.006 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7420 (tm-30) cc_final: 0.6656 (tm-30) REVERT: a 211 MET cc_start: 0.7453 (mmm) cc_final: 0.7196 (mtp) REVERT: a 225 LYS cc_start: 0.8652 (tttt) cc_final: 0.8286 (mmtp) REVERT: a 283 GLN cc_start: 0.7327 (tm-30) cc_final: 0.6487 (tm-30) REVERT: a 296 LYS cc_start: 0.8393 (tppt) cc_final: 0.7714 (mttm) REVERT: C 34 GLU cc_start: 0.7173 (mp0) cc_final: 0.6326 (mp0) REVERT: C 50 ASN cc_start: 0.6857 (m110) cc_final: 0.6579 (m110) REVERT: c 122 MET cc_start: 0.6005 (ptt) cc_final: 0.5539 (ppp) REVERT: c 164 GLU cc_start: 0.6592 (tp30) cc_final: 0.6252 (tp30) REVERT: c 176 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7236 (mttt) outliers start: 35 outliers final: 28 residues processed: 240 average time/residue: 0.1585 time to fit residues: 49.5474 Evaluate side-chains 246 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 272 SER Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 388 THR Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 0.0770 chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 322 HIS C 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6450 Z= 0.240 Angle : 0.692 10.944 8682 Z= 0.343 Chirality : 0.046 0.232 964 Planarity : 0.004 0.058 1122 Dihedral : 5.458 58.410 844 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.87 % Allowed : 26.04 % Favored : 69.08 % 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: -1.64 (0.28), residues: 776 helix: 0.68 (0.42), residues: 138 sheet: -1.29 (0.44), residues: 140 loop : -1.62 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 294 HIS 0.009 0.001 HIS b 322 PHE 0.030 0.002 PHE B 370 TYR 0.013 0.001 TYR C 37 ARG 0.004 0.000 ARG a 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.471 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 283 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6636 (tm-30) REVERT: a 211 MET cc_start: 0.7445 (mmm) cc_final: 0.7197 (mtp) REVERT: a 225 LYS cc_start: 0.8662 (tttt) cc_final: 0.8275 (mmtp) REVERT: a 283 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6459 (tm-30) REVERT: a 296 LYS cc_start: 0.8326 (tppt) cc_final: 0.7655 (mttm) REVERT: C 34 GLU cc_start: 0.7241 (mp0) cc_final: 0.6944 (mp0) REVERT: C 50 ASN cc_start: 0.6773 (m110) cc_final: 0.6498 (m110) REVERT: c 122 MET cc_start: 0.6065 (ptt) cc_final: 0.5539 (ppp) REVERT: c 164 GLU cc_start: 0.6593 (tp30) cc_final: 0.6300 (tp30) REVERT: c 176 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7244 (mttt) outliers start: 35 outliers final: 32 residues processed: 236 average time/residue: 0.1577 time to fit residues: 48.2333 Evaluate side-chains 247 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 276 LYS Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 366 VAL Chi-restraints excluded: chain b residue 388 THR Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 157 GLU Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 20 optimal weight: 0.0770 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 322 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6450 Z= 0.228 Angle : 0.690 10.487 8682 Z= 0.341 Chirality : 0.046 0.225 964 Planarity : 0.005 0.058 1122 Dihedral : 5.439 59.029 844 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.32 % Allowed : 27.02 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.29), residues: 776 helix: 0.72 (0.42), residues: 138 sheet: -1.31 (0.45), residues: 136 loop : -1.53 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 294 HIS 0.015 0.001 HIS b 322 PHE 0.015 0.001 PHE b 327 TYR 0.013 0.001 TYR C 37 ARG 0.004 0.000 ARG a 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8071 (t0) cc_final: 0.7840 (t0) REVERT: A 283 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 370 PHE cc_start: 0.7112 (m-10) cc_final: 0.6899 (m-10) REVERT: B 374 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6793 (mtm110) REVERT: a 225 LYS cc_start: 0.8664 (tttt) cc_final: 0.8281 (mmtp) REVERT: a 283 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6483 (tm-30) REVERT: a 296 LYS cc_start: 0.8314 (tppt) cc_final: 0.7662 (mttm) REVERT: C 34 GLU cc_start: 0.7265 (mp0) cc_final: 0.6967 (mp0) REVERT: C 50 ASN cc_start: 0.6751 (m110) cc_final: 0.6463 (m110) REVERT: c 122 MET cc_start: 0.6097 (ptt) cc_final: 0.5565 (ppp) REVERT: c 140 ARG cc_start: 0.8511 (mpt90) cc_final: 0.8137 (mmt180) REVERT: c 164 GLU cc_start: 0.6559 (tp30) cc_final: 0.6294 (tp30) REVERT: c 176 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7249 (mttt) outliers start: 31 outliers final: 30 residues processed: 228 average time/residue: 0.2028 time to fit residues: 59.7341 Evaluate side-chains 242 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 276 LYS Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 366 VAL Chi-restraints excluded: chain b residue 388 THR Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 322 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6450 Z= 0.241 Angle : 0.710 10.695 8682 Z= 0.351 Chirality : 0.047 0.219 964 Planarity : 0.005 0.058 1122 Dihedral : 5.438 59.375 844 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.60 % Allowed : 27.02 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.29), residues: 776 helix: 0.75 (0.42), residues: 138 sheet: -1.37 (0.45), residues: 136 loop : -1.53 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 294 HIS 0.014 0.001 HIS b 322 PHE 0.015 0.001 PHE b 327 TYR 0.014 0.001 TYR c 156 ARG 0.007 0.000 ARG C 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7466 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 370 PHE cc_start: 0.7190 (m-10) cc_final: 0.6980 (m-10) REVERT: B 374 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6722 (mtm110) REVERT: a 225 LYS cc_start: 0.8663 (tttt) cc_final: 0.8278 (mmtp) REVERT: a 283 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6464 (tm-30) REVERT: a 296 LYS cc_start: 0.8311 (tppt) cc_final: 0.7659 (mttm) REVERT: C 34 GLU cc_start: 0.7249 (mp0) cc_final: 0.6955 (mp0) REVERT: C 50 ASN cc_start: 0.6099 (m110) cc_final: 0.5812 (m110) REVERT: c 122 MET cc_start: 0.6113 (ptt) cc_final: 0.5570 (ppp) REVERT: c 164 GLU cc_start: 0.6615 (tp30) cc_final: 0.6362 (tp30) REVERT: c 176 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7233 (mttt) outliers start: 33 outliers final: 32 residues processed: 233 average time/residue: 0.2010 time to fit residues: 60.1467 Evaluate side-chains 249 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 269 ASN Chi-restraints excluded: chain a residue 276 LYS Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 348 VAL Chi-restraints excluded: chain b residue 366 VAL Chi-restraints excluded: chain b residue 388 THR Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain c residue 108 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0770 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.225659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154902 restraints weight = 5881.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163562 restraints weight = 2699.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169474 restraints weight = 1717.478| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6450 Z= 0.190 Angle : 0.716 10.676 8682 Z= 0.350 Chirality : 0.047 0.212 964 Planarity : 0.004 0.057 1122 Dihedral : 5.284 58.757 844 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.62 % Allowed : 28.41 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.29), residues: 776 helix: 0.80 (0.42), residues: 138 sheet: -1.33 (0.46), residues: 136 loop : -1.42 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 294 HIS 0.007 0.001 HIS b 322 PHE 0.015 0.001 PHE a 231 TYR 0.012 0.001 TYR C 37 ARG 0.007 0.001 ARG C 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.93 seconds wall clock time: 45 minutes 10.53 seconds (2710.53 seconds total)