Starting phenix.real_space_refine on Thu Jul 24 13:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_40781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_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/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_40781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_40781.map" model { file = "/net/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_40781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sv1_40781/07_2025/8sv1_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-5711/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: 4.59, per 1000 atoms: 0.73 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: 1.33 Conformation dependent library (CDL) restraints added in 831.4 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: 0.74 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: 1.85 Time building geometry restraints manager: 1.62 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: 0.01 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: 1.160 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.650 Find NCS groups from input model: 0.230 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- 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= 0.176 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 Details of bonding type rmsd hydrogen bonds : bond 0.22246 ( 187) hydrogen bonds : angle 8.10325 ( 519) covalent geometry : bond 0.00337 ( 6450) covalent geometry : angle 0.75463 ( 8682) *********************** 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 : 0.727 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: 0.2048 time to fit residues: 67.1175 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 : 0.691 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.228508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157187 restraints weight = 6139.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.165713 restraints weight = 2844.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.170923 restraints weight = 1817.183| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 187) hydrogen bonds : angle 5.51768 ( 519) covalent geometry : bond 0.00349 ( 6450) covalent geometry : angle 0.63775 ( 8682) *********************** 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 : 0.720 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: 0.7494 (mp10) cc_final: 0.7204 (mp10) REVERT: A 283 GLN cc_start: 0.7469 (tm-30) cc_final: 0.6421 (tm-30) REVERT: a 225 LYS cc_start: 0.8991 (tttt) cc_final: 0.8395 (mmtp) REVERT: a 241 GLU cc_start: 0.8475 (mp0) cc_final: 0.8202 (mp0) REVERT: a 283 GLN cc_start: 0.7422 (tm-30) cc_final: 0.6313 (tm-30) REVERT: a 296 LYS cc_start: 0.8460 (tppt) cc_final: 0.7675 (mttt) REVERT: C 50 ASN cc_start: 0.7017 (m110) cc_final: 0.6673 (m110) REVERT: C 164 GLU cc_start: 0.5098 (tp30) cc_final: 0.4782 (tp30) REVERT: c 50 ASN cc_start: 0.6795 (m110) cc_final: 0.6455 (m110) REVERT: c 176 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8215 (mtmt) outliers start: 21 outliers final: 16 residues processed: 227 average time/residue: 0.2110 time to fit residues: 60.8903 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 : 0.729 ------------------------------------------------------------------------------- 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 59 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 C 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.219459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147713 restraints weight = 6368.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155058 restraints weight = 3164.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159654 restraints weight = 2130.969| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 6450 Z= 0.341 Angle : 0.739 7.069 8682 Z= 0.393 Chirality : 0.050 0.277 964 Planarity : 0.006 0.058 1122 Dihedral : 6.747 56.230 852 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.74 % Allowed : 22.14 % Favored : 73.12 % 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: -1.86 (0.28), residues: 776 helix: 0.54 (0.42), residues: 138 sheet: -0.90 (0.44), residues: 140 loop : -1.96 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP b 340 HIS 0.007 0.002 HIS B 322 PHE 0.019 0.002 PHE b 327 TYR 0.014 0.002 TYR C 37 ARG 0.007 0.001 ARG b 352 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 187) hydrogen bonds : angle 5.30980 ( 519) covalent geometry : bond 0.00775 ( 6450) covalent geometry : angle 0.73859 ( 8682) *********************** 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 274 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 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: A 171 GLU cc_start: 0.7361 (tt0) cc_final: 0.6791 (tt0) REVERT: A 283 GLN cc_start: 0.7599 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 374 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6536 (mtm110) REVERT: a 225 LYS cc_start: 0.8946 (tttt) cc_final: 0.8391 (mmtp) REVERT: a 241 GLU cc_start: 0.8579 (mp0) cc_final: 0.8295 (mp0) REVERT: a 250 GLU cc_start: 0.8005 (pm20) cc_final: 0.7530 (pm20) REVERT: a 251 GLN cc_start: 0.7943 (mt0) cc_final: 0.7640 (mp10) REVERT: a 283 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6767 (tm-30) REVERT: a 296 LYS cc_start: 0.8454 (tppt) cc_final: 0.7675 (mttt) REVERT: b 322 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7255 (m-70) REVERT: b 374 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6479 (mtm110) REVERT: C 34 GLU cc_start: 0.7066 (mp0) cc_final: 0.6806 (mp0) REVERT: C 50 ASN cc_start: 0.7190 (m110) cc_final: 0.6888 (m110) REVERT: C 164 GLU cc_start: 0.5490 (tp30) cc_final: 0.5205 (tp30) REVERT: c 34 GLU cc_start: 0.7025 (mp0) cc_final: 0.6777 (mp0) REVERT: c 50 ASN cc_start: 0.5977 (m110) cc_final: 0.5638 (m110) outliers start: 34 outliers final: 26 residues processed: 256 average time/residue: 0.2038 time to fit residues: 66.3457 Evaluate side-chains 256 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 374 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain a residue 212 THR 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 374 ARG Chi-restraints excluded: chain b residue 383 ARG Chi-restraints excluded: chain b residue 388 THR 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 82 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.226035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154959 restraints weight = 6324.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.163443 restraints weight = 2886.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.168783 restraints weight = 1842.816| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2909 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= 0.129 Angle : 0.633 8.093 8682 Z= 0.323 Chirality : 0.046 0.256 964 Planarity : 0.004 0.056 1122 Dihedral : 6.326 59.082 852 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.04 % Allowed : 24.09 % Favored : 71.87 % 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: -1.62 (0.28), residues: 776 helix: 0.62 (0.42), residues: 138 sheet: -0.90 (0.44), residues: 140 loop : -1.72 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 340 HIS 0.003 0.001 HIS A 248 PHE 0.014 0.001 PHE b 327 TYR 0.015 0.001 TYR C 37 ARG 0.004 0.000 ARG a 163 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 187) hydrogen bonds : angle 4.87841 ( 519) covalent geometry : bond 0.00294 ( 6450) covalent geometry : angle 0.63294 ( 8682) *********************** 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 253 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.796 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: 0.7422 (tm-30) cc_final: 0.6366 (tm-30) REVERT: B 370 PHE cc_start: 0.7849 (m-10) cc_final: 0.7636 (m-10) REVERT: a 225 LYS cc_start: 0.8928 (tttt) cc_final: 0.8333 (mttm) REVERT: a 241 GLU cc_start: 0.8514 (mp0) cc_final: 0.8238 (mp0) REVERT: a 283 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6460 (tm-30) REVERT: a 296 LYS cc_start: 0.8446 (tppt) cc_final: 0.7682 (mttm) REVERT: b 370 PHE cc_start: 0.7892 (m-10) cc_final: 0.7638 (m-10) REVERT: C 34 GLU cc_start: 0.6955 (mp0) cc_final: 0.5916 (mp0) REVERT: C 50 ASN cc_start: 0.7060 (m110) cc_final: 0.6746 (m110) REVERT: c 34 GLU cc_start: 0.6937 (mp0) cc_final: 0.6503 (mp0) REVERT: c 184 SER cc_start: 0.5672 (OUTLIER) cc_final: 0.5467 (p) outliers start: 29 outliers final: 24 residues processed: 239 average time/residue: 0.2333 time to fit residues: 71.7376 Evaluate side-chains 240 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 348 VAL 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 249 SER Chi-restraints excluded: chain b residue 322 HIS Chi-restraints excluded: chain b residue 334 THR 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 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 160 PHE Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain c residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.214241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139627 restraints weight = 6099.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147263 restraints weight = 3002.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152205 restraints weight = 1980.849| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6450 Z= 0.295 Angle : 0.742 8.247 8682 Z= 0.386 Chirality : 0.049 0.265 964 Planarity : 0.005 0.058 1122 Dihedral : 6.504 58.567 848 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.82 % Allowed : 23.68 % Favored : 69.50 % 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: -2.05 (0.27), residues: 776 helix: 0.40 (0.42), residues: 138 sheet: -1.41 (0.42), residues: 140 loop : -1.96 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP b 340 HIS 0.006 0.002 HIS B 322 PHE 0.026 0.002 PHE b 327 TYR 0.016 0.002 TYR C 156 ARG 0.004 0.001 ARG b 383 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 187) hydrogen bonds : angle 5.02441 ( 519) covalent geometry : bond 0.00670 ( 6450) covalent geometry : angle 0.74209 ( 8682) *********************** 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 278 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7318 (tt0) cc_final: 0.6635 (tt0) REVERT: A 283 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6413 (tm-30) REVERT: B 370 PHE cc_start: 0.8080 (m-10) cc_final: 0.7165 (m-10) REVERT: B 374 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6231 (mtm110) REVERT: a 225 LYS cc_start: 0.8983 (tttt) cc_final: 0.8296 (mmtp) REVERT: a 241 GLU cc_start: 0.8652 (mp0) cc_final: 0.8279 (mp0) REVERT: a 283 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6630 (tm-30) REVERT: a 296 LYS cc_start: 0.8357 (tppt) cc_final: 0.7614 (mttm) REVERT: b 322 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7042 (m170) REVERT: b 370 PHE cc_start: 0.8021 (m-10) cc_final: 0.7608 (m-10) REVERT: C 34 GLU cc_start: 0.7033 (mp0) cc_final: 0.5890 (mp0) REVERT: C 50 ASN cc_start: 0.6989 (m110) cc_final: 0.6715 (m110) REVERT: c 176 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7012 (mttt) outliers start: 49 outliers final: 30 residues processed: 256 average time/residue: 0.2131 time to fit residues: 69.8732 Evaluate side-chains 260 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL 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 388 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain a residue 156 MET 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 a residue 272 SER 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 389 THR Chi-restraints excluded: chain b residue 393 THR 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 108 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 176 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 44 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.217661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143838 restraints weight = 6039.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151867 restraints weight = 2861.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157276 restraints weight = 1871.711| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6450 Z= 0.208 Angle : 0.715 8.933 8682 Z= 0.367 Chirality : 0.048 0.269 964 Planarity : 0.005 0.057 1122 Dihedral : 5.139 24.032 840 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.87 % Allowed : 26.60 % Favored : 68.52 % 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: -1.94 (0.28), residues: 776 helix: 0.43 (0.42), residues: 138 sheet: -1.42 (0.43), residues: 140 loop : -1.84 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 340 HIS 0.005 0.001 HIS A 248 PHE 0.020 0.002 PHE b 327 TYR 0.013 0.002 TYR C 156 ARG 0.003 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 187) hydrogen bonds : angle 4.88417 ( 519) covalent geometry : bond 0.00480 ( 6450) covalent geometry : angle 0.71458 ( 8682) *********************** 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 261 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.581 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 172 GLU cc_start: 0.8073 (tt0) cc_final: 0.7673 (mp0) REVERT: A 283 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6365 (tm-30) REVERT: B 370 PHE cc_start: 0.8003 (m-10) cc_final: 0.7715 (m-10) REVERT: a 225 LYS cc_start: 0.8966 (tttt) cc_final: 0.8280 (mmtp) REVERT: a 241 GLU cc_start: 0.8597 (mp0) cc_final: 0.8250 (mp0) REVERT: a 283 GLN cc_start: 0.7332 (tm-30) cc_final: 0.6197 (tm-30) REVERT: a 296 LYS cc_start: 0.8360 (tppt) cc_final: 0.7622 (mttm) REVERT: b 322 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6799 (m170) REVERT: b 370 PHE cc_start: 0.7914 (m-10) cc_final: 0.7587 (m-10) REVERT: C 34 GLU cc_start: 0.7105 (mp0) cc_final: 0.5979 (mp0) REVERT: C 50 ASN cc_start: 0.6816 (m110) cc_final: 0.6499 (m110) REVERT: c 122 MET cc_start: 0.5784 (ptt) cc_final: 0.5228 (ppp) REVERT: c 174 LEU cc_start: 0.9029 (tt) cc_final: 0.8743 (tp) outliers start: 35 outliers final: 29 residues processed: 248 average time/residue: 0.1893 time to fit residues: 60.6932 Evaluate side-chains 252 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 B residue 400 LEU Chi-restraints excluded: chain a residue 171 GLU Chi-restraints excluded: chain a residue 249 SER 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 84 ILE Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 108 SER 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 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 0.0040 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147948 restraints weight = 5998.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.156751 restraints weight = 2754.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162434 restraints weight = 1761.990| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3800 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= 0.133 Angle : 0.684 9.188 8682 Z= 0.345 Chirality : 0.046 0.245 964 Planarity : 0.004 0.057 1122 Dihedral : 4.780 22.990 840 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.46 % Allowed : 27.30 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.28), residues: 776 helix: 0.54 (0.42), residues: 138 sheet: -1.29 (0.45), residues: 136 loop : -1.60 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 340 HIS 0.004 0.001 HIS A 248 PHE 0.015 0.001 PHE b 327 TYR 0.015 0.001 TYR C 156 ARG 0.009 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 187) hydrogen bonds : angle 4.71108 ( 519) covalent geometry : bond 0.00305 ( 6450) covalent geometry : angle 0.68359 ( 8682) *********************** 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 254 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8037 (tt0) cc_final: 0.7608 (mp0) REVERT: A 283 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6349 (tm-30) REVERT: B 370 PHE cc_start: 0.7916 (m-10) cc_final: 0.7679 (m-10) REVERT: B 383 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7233 (mmt-90) REVERT: a 179 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7790 (ttp80) REVERT: a 225 LYS cc_start: 0.8936 (tttt) cc_final: 0.8274 (mttm) REVERT: a 241 GLU cc_start: 0.8560 (mp0) cc_final: 0.8250 (mp0) REVERT: a 283 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6051 (tm-30) REVERT: a 296 LYS cc_start: 0.8398 (tppt) cc_final: 0.7639 (mttm) REVERT: b 370 PHE cc_start: 0.7864 (m-10) cc_final: 0.7529 (m-10) REVERT: C 34 GLU cc_start: 0.7091 (mp0) cc_final: 0.5890 (mp0) REVERT: C 50 ASN cc_start: 0.6900 (m110) cc_final: 0.6543 (m110) REVERT: c 122 MET cc_start: 0.5773 (ptt) cc_final: 0.5171 (ppp) outliers start: 32 outliers final: 27 residues processed: 238 average time/residue: 0.2728 time to fit residues: 83.8288 Evaluate side-chains 245 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 233 VAL 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 383 ARG Chi-restraints excluded: chain B residue 388 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 249 SER 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 366 VAL Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 160 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 157 GLU 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 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 23 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.221776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145166 restraints weight = 6017.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153824 restraints weight = 2813.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159516 restraints weight = 1824.217| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3930 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= 0.151 Angle : 0.707 10.779 8682 Z= 0.352 Chirality : 0.047 0.239 964 Planarity : 0.004 0.057 1122 Dihedral : 4.785 23.212 840 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.60 % Allowed : 26.88 % Favored : 68.52 % 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: -1.75 (0.28), residues: 776 helix: 0.54 (0.42), residues: 138 sheet: -1.44 (0.44), residues: 136 loop : -1.65 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 340 HIS 0.005 0.001 HIS A 237 PHE 0.016 0.001 PHE b 327 TYR 0.013 0.001 TYR C 156 ARG 0.005 0.000 ARG a 163 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 187) hydrogen bonds : angle 4.67269 ( 519) covalent geometry : bond 0.00349 ( 6450) covalent geometry : angle 0.70750 ( 8682) *********************** 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 260 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7371 (tm-30) cc_final: 0.6324 (tm-30) REVERT: B 352 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7975 (tpp80) REVERT: B 370 PHE cc_start: 0.7951 (m-10) cc_final: 0.7696 (m-10) REVERT: B 383 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7332 (mmt-90) REVERT: a 225 LYS cc_start: 0.8948 (tttt) cc_final: 0.8157 (mmtp) REVERT: a 241 GLU cc_start: 0.8585 (mp0) cc_final: 0.8253 (mp0) REVERT: a 283 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6128 (tm-30) REVERT: a 296 LYS cc_start: 0.8316 (tppt) cc_final: 0.7580 (mttm) REVERT: b 370 PHE cc_start: 0.7893 (m-10) cc_final: 0.7545 (m-10) REVERT: C 34 GLU cc_start: 0.7151 (mp0) cc_final: 0.5855 (mp0) REVERT: C 50 ASN cc_start: 0.6623 (m110) cc_final: 0.6240 (m110) REVERT: C 176 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.5963 (mttt) REVERT: c 34 GLU cc_start: 0.6977 (mp0) cc_final: 0.6470 (mp0) REVERT: c 122 MET cc_start: 0.5761 (ptt) cc_final: 0.5160 (ppp) outliers start: 33 outliers final: 27 residues processed: 243 average time/residue: 0.2365 time to fit residues: 75.0741 Evaluate side-chains 252 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 233 VAL 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 383 ARG 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 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 369 ILE Chi-restraints excluded: chain b residue 389 THR Chi-restraints excluded: chain b residue 393 THR 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 46 SER Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 142 VAL 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 14 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.225919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151310 restraints weight = 6040.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160587 restraints weight = 2687.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.166704 restraints weight = 1686.472| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4066 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= 0.124 Angle : 0.691 9.771 8682 Z= 0.342 Chirality : 0.046 0.219 964 Planarity : 0.004 0.057 1122 Dihedral : 4.585 21.365 840 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.76 % Allowed : 27.99 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.29), residues: 776 helix: 0.68 (0.42), residues: 138 sheet: -1.36 (0.45), residues: 136 loop : -1.52 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 340 HIS 0.004 0.001 HIS A 237 PHE 0.012 0.001 PHE b 327 TYR 0.013 0.001 TYR C 156 ARG 0.005 0.000 ARG a 163 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 187) hydrogen bonds : angle 4.57521 ( 519) covalent geometry : bond 0.00287 ( 6450) covalent geometry : angle 0.69111 ( 8682) *********************** 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 245 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6373 (tm-30) REVERT: B 370 PHE cc_start: 0.7919 (m-10) cc_final: 0.7665 (m-10) REVERT: B 383 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7255 (mmt-90) REVERT: a 211 MET cc_start: 0.8145 (mmm) cc_final: 0.7823 (mtp) REVERT: a 225 LYS cc_start: 0.8935 (tttt) cc_final: 0.8266 (mttm) REVERT: a 241 GLU cc_start: 0.8577 (mp0) cc_final: 0.8225 (mp0) REVERT: a 275 ASP cc_start: 0.8796 (t0) cc_final: 0.8580 (t0) REVERT: a 283 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6162 (tm-30) REVERT: a 296 LYS cc_start: 0.8326 (tppt) cc_final: 0.7565 (mttm) REVERT: b 370 PHE cc_start: 0.7874 (m-10) cc_final: 0.7551 (m-10) REVERT: C 34 GLU cc_start: 0.7172 (mp0) cc_final: 0.5878 (mp0) REVERT: c 34 GLU cc_start: 0.7003 (mp0) cc_final: 0.6507 (mp0) REVERT: c 122 MET cc_start: 0.5757 (ptt) cc_final: 0.5145 (ppp) REVERT: c 140 ARG cc_start: 0.8255 (mpt90) cc_final: 0.7941 (mmt180) REVERT: c 176 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7595 (mtmt) outliers start: 27 outliers final: 24 residues processed: 234 average time/residue: 0.3113 time to fit residues: 96.1966 Evaluate side-chains 240 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 VAL 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 383 ARG 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 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 389 THR Chi-restraints excluded: chain b residue 393 THR 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 160 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 84 ILE 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 47 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.223820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146333 restraints weight = 6021.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.155216 restraints weight = 2817.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160947 restraints weight = 1826.641| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4152 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= 0.156 Angle : 0.726 9.761 8682 Z= 0.361 Chirality : 0.047 0.217 964 Planarity : 0.005 0.057 1122 Dihedral : 4.641 22.425 840 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.62 % Allowed : 28.69 % Favored : 67.69 % 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: -1.59 (0.29), residues: 776 helix: 0.71 (0.42), residues: 138 sheet: -1.36 (0.46), residues: 136 loop : -1.54 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 340 HIS 0.003 0.001 HIS A 248 PHE 0.015 0.001 PHE b 327 TYR 0.023 0.001 TYR C 156 ARG 0.009 0.001 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 187) hydrogen bonds : angle 4.64778 ( 519) covalent geometry : bond 0.00362 ( 6450) covalent geometry : angle 0.72596 ( 8682) ********************** 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 247 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6331 (tm-30) REVERT: B 370 PHE cc_start: 0.7983 (m-10) cc_final: 0.7694 (m-10) REVERT: B 383 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7101 (mmt-90) REVERT: a 225 LYS cc_start: 0.8943 (tttt) cc_final: 0.8194 (mmtp) REVERT: a 241 GLU cc_start: 0.8583 (mp0) cc_final: 0.8228 (mp0) REVERT: a 283 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6109 (tm-30) REVERT: a 296 LYS cc_start: 0.8299 (tppt) cc_final: 0.7548 (mttm) REVERT: b 370 PHE cc_start: 0.7904 (m-10) cc_final: 0.7568 (m-10) REVERT: C 34 GLU cc_start: 0.7227 (mp0) cc_final: 0.6610 (mp0) REVERT: C 140 ARG cc_start: 0.8338 (mtt90) cc_final: 0.8127 (mpt90) REVERT: c 34 GLU cc_start: 0.7087 (mp0) cc_final: 0.6595 (mp0) REVERT: c 122 MET cc_start: 0.5822 (ptt) cc_final: 0.5192 (ppp) REVERT: c 140 ARG cc_start: 0.8173 (mpt90) cc_final: 0.7767 (mmt180) REVERT: c 176 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7692 (mtmt) outliers start: 26 outliers final: 25 residues processed: 236 average time/residue: 0.4582 time to fit residues: 136.3482 Evaluate side-chains 243 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 289 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 383 ARG 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 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 389 THR Chi-restraints excluded: chain b residue 393 THR 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 160 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 84 ILE 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 65 optimal weight: 0.0040 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.224975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.149015 restraints weight = 6109.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158342 restraints weight = 2746.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164262 restraints weight = 1734.088| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6450 Z= 0.130 Angle : 0.721 9.922 8682 Z= 0.353 Chirality : 0.047 0.207 964 Planarity : 0.004 0.057 1122 Dihedral : 4.553 21.103 840 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.34 % Allowed : 29.53 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.29), residues: 776 helix: 0.74 (0.42), residues: 138 sheet: -1.35 (0.46), residues: 136 loop : -1.46 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 340 HIS 0.003 0.001 HIS A 237 PHE 0.011 0.001 PHE b 327 TYR 0.023 0.001 TYR C 156 ARG 0.007 0.000 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 187) hydrogen bonds : angle 4.62882 ( 519) covalent geometry : bond 0.00299 ( 6450) covalent geometry : angle 0.72126 ( 8682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3799.97 seconds wall clock time: 70 minutes 42.39 seconds (4242.39 seconds total)