Starting phenix.real_space_refine on Wed Feb 12 09:39:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2n_38858/02_2025/8y2n_38858.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.087 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 5198 2.51 5 N 1204 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2674 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "B" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1089 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'6PL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6PL:plan-1': 2, '6PL:plan-2': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'6PL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: D, C Time building chain proxies: 7.31, per 1000 atoms: 0.95 Number of scatterers: 7714 At special positions: 0 Unit cell: (121.136, 97.552, 99.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1272 8.00 N 1204 7.00 C 5198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 67.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 84 through 101 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 129 through 160 removed outlier: 3.970A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 167 through 196 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 248 through 269 removed outlier: 3.627A pdb=" N PHE A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 Processing helix chain 'A' and resid 301 through 335 removed outlier: 4.509A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 384 removed outlier: 4.363A pdb=" N ILE A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 47 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.841A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.633A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 84 through 101 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 129 through 160 removed outlier: 3.970A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 167 through 196 Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'C' and resid 248 through 269 removed outlier: 3.628A pdb=" N PHE C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 297 Processing helix chain 'C' and resid 301 through 335 removed outlier: 4.508A pdb=" N PHE C 305 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 384 removed outlier: 4.363A pdb=" N ILE C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 47 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.840A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.633A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 54 through 59 removed outlier: 3.555A pdb=" N THR B 54 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA B 69 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR B 125 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 100 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 54 through 59 removed outlier: 3.557A pdb=" N THR D 54 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA D 69 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR D 125 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 100 " --> pdb=" O GLY D 130 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1098 1.28 - 1.41: 2413 1.41 - 1.54: 4274 1.54 - 1.67: 117 1.67 - 1.80: 58 Bond restraints: 7960 Sorted by residual: bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.531 1.444 0.088 1.08e-02 8.57e+03 6.57e+01 bond pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 1.531 1.444 0.087 1.08e-02 8.57e+03 6.48e+01 bond pdb=" CA ASN A 203 " pdb=" C ASN A 203 " ideal model delta sigma weight residual 1.528 1.422 0.105 1.32e-02 5.74e+03 6.33e+01 bond pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 1.528 1.422 0.105 1.32e-02 5.74e+03 6.33e+01 bond pdb=" CA PHE C 201 " pdb=" C PHE C 201 " ideal model delta sigma weight residual 1.527 1.438 0.089 1.30e-02 5.92e+03 4.71e+01 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 10342 2.90 - 5.81: 371 5.81 - 8.71: 33 8.71 - 11.62: 10 11.62 - 14.52: 8 Bond angle restraints: 10764 Sorted by residual: angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 114.04 102.26 11.78 1.24e+00 6.50e-01 9.02e+01 angle pdb=" N LEU C 162 " pdb=" CA LEU C 162 " pdb=" C LEU C 162 " ideal model delta sigma weight residual 114.04 102.34 11.70 1.24e+00 6.50e-01 8.90e+01 angle pdb=" N PHE C 201 " pdb=" CA PHE C 201 " pdb=" C PHE C 201 " ideal model delta sigma weight residual 111.39 123.75 -12.36 1.38e+00 5.25e-01 8.02e+01 angle pdb=" N PHE A 201 " pdb=" CA PHE A 201 " pdb=" C PHE A 201 " ideal model delta sigma weight residual 111.39 123.73 -12.34 1.38e+00 5.25e-01 8.00e+01 angle pdb=" N SER A 166 " pdb=" CA SER A 166 " pdb=" C SER A 166 " ideal model delta sigma weight residual 110.80 98.72 12.08 2.13e+00 2.20e-01 3.22e+01 ... (remaining 10759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3999 17.69 - 35.37: 466 35.37 - 53.06: 87 53.06 - 70.75: 38 70.75 - 88.43: 8 Dihedral angle restraints: 4598 sinusoidal: 1928 harmonic: 2670 Sorted by residual: dihedral pdb=" C PHE A 201 " pdb=" N PHE A 201 " pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " ideal model delta harmonic sigma weight residual -122.60 -155.63 33.03 0 2.50e+00 1.60e-01 1.75e+02 dihedral pdb=" C PHE C 201 " pdb=" N PHE C 201 " pdb=" CA PHE C 201 " pdb=" CB PHE C 201 " ideal model delta harmonic sigma weight residual -122.60 -155.61 33.01 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" N PHE A 201 " pdb=" C PHE A 201 " pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " ideal model delta harmonic sigma weight residual 122.80 155.76 -32.96 0 2.50e+00 1.60e-01 1.74e+02 ... (remaining 4595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 1132 0.326 - 0.652: 6 0.652 - 0.978: 0 0.978 - 1.304: 0 1.304 - 1.630: 2 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA PHE C 201 " pdb=" N PHE C 201 " pdb=" C PHE C 201 " pdb=" CB PHE C 201 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.65e+01 chirality pdb=" CA PHE A 201 " pdb=" N PHE A 201 " pdb=" C PHE A 201 " pdb=" CB PHE A 201 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.64e+01 chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1137 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 201 " 0.046 2.00e-02 2.50e+03 3.54e-02 2.19e+01 pdb=" CG PHE C 201 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE C 201 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 201 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 201 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 201 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 201 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 201 " -0.046 2.00e-02 2.50e+03 3.52e-02 2.17e+01 pdb=" CG PHE A 201 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 201 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 201 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 201 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 201 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 106 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C LYS C 106 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS C 106 " 0.020 2.00e-02 2.50e+03 pdb=" N THR C 107 " 0.018 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 6762 3.16 - 3.74: 11804 3.74 - 4.32: 16487 4.32 - 4.90: 27540 Nonbonded interactions: 62678 Sorted by model distance: nonbonded pdb=" O THR A 204 " pdb=" N ALA A 206 " model vdw 1.998 3.120 nonbonded pdb=" O THR C 204 " pdb=" N ALA C 206 " model vdw 1.999 3.120 nonbonded pdb=" SG CYS D 102 " pdb=" SG CYS D 142 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS D 53 " pdb=" SG CYS D 75 " model vdw 2.028 3.760 nonbonded pdb=" OH TYR A 224 " pdb=" OG SER A 266 " model vdw 2.041 3.040 ... (remaining 62673 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.450 Find NCS groups from input model: 0.140 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.011 0.118 7960 Z= 0.717 Angle : 1.213 14.522 10764 Z= 0.686 Chirality : 0.096 1.630 1140 Planarity : 0.006 0.050 1298 Dihedral : 15.982 88.432 2880 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 1.58 % Allowed : 6.76 % Favored : 91.67 % Rotamer: Outliers : 2.96 % Allowed : 3.21 % Favored : 93.83 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 888 helix: 0.49 (0.22), residues: 556 sheet: -0.40 (0.73), residues: 58 loop : -2.40 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 200 HIS 0.008 0.002 HIS A 111 PHE 0.080 0.003 PHE C 201 TYR 0.023 0.002 TYR D 114 ARG 0.006 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6931 (mmt) cc_final: 0.6707 (mtt) REVERT: A 177 MET cc_start: 0.6893 (mmt) cc_final: 0.6231 (tpt) REVERT: A 193 CYS cc_start: 0.7390 (t) cc_final: 0.6802 (m) REVERT: A 375 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5128 (mm) REVERT: A 377 ARG cc_start: 0.6510 (ttp-170) cc_final: 0.5528 (tpt90) REVERT: C 89 MET cc_start: 0.6967 (mmt) cc_final: 0.6751 (mtt) REVERT: C 177 MET cc_start: 0.6838 (mmt) cc_final: 0.6173 (tpt) REVERT: C 193 CYS cc_start: 0.7383 (t) cc_final: 0.6821 (m) REVERT: C 375 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.5127 (mm) REVERT: C 377 ARG cc_start: 0.6486 (ttp-170) cc_final: 0.5573 (tpt90) REVERT: D 136 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7678 (tp30) outliers start: 24 outliers final: 2 residues processed: 155 average time/residue: 0.2358 time to fit residues: 46.9302 Evaluate side-chains 106 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 338 ASN A 365 GLN C 163 HIS C 338 ASN C 365 GLN D 149 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132197 restraints weight = 9498.615| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.21 r_work: 0.3400 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7960 Z= 0.267 Angle : 0.708 8.687 10764 Z= 0.388 Chirality : 0.048 0.260 1140 Planarity : 0.006 0.050 1298 Dihedral : 11.241 61.179 1173 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.36 % Rotamer: Outliers : 2.47 % Allowed : 9.88 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 888 helix: 0.80 (0.22), residues: 560 sheet: -0.30 (0.66), residues: 58 loop : -2.14 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 68 HIS 0.018 0.002 HIS A 163 PHE 0.020 0.001 PHE C 135 TYR 0.039 0.002 TYR C 182 ARG 0.003 0.001 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.833 Fit side-chains REVERT: A 177 MET cc_start: 0.7328 (mmt) cc_final: 0.6669 (tpt) REVERT: A 193 CYS cc_start: 0.7560 (t) cc_final: 0.6999 (m) REVERT: A 371 TRP cc_start: 0.6023 (OUTLIER) cc_final: 0.5363 (m-90) REVERT: A 375 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.5917 (mt) REVERT: A 377 ARG cc_start: 0.6690 (ttp-170) cc_final: 0.5824 (tpt90) REVERT: B 134 ASP cc_start: 0.8573 (p0) cc_final: 0.8303 (p0) REVERT: C 89 MET cc_start: 0.7489 (mmt) cc_final: 0.7283 (mtt) REVERT: C 177 MET cc_start: 0.7317 (mmt) cc_final: 0.6650 (tpt) REVERT: C 193 CYS cc_start: 0.7511 (t) cc_final: 0.7010 (m) REVERT: C 205 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7322 (tptt) REVERT: C 371 TRP cc_start: 0.6025 (OUTLIER) cc_final: 0.5329 (m-90) REVERT: C 375 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.5901 (mt) REVERT: C 377 ARG cc_start: 0.6770 (ttp-170) cc_final: 0.5851 (tpt90) REVERT: D 134 ASP cc_start: 0.8588 (p0) cc_final: 0.8324 (p0) REVERT: D 136 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8086 (tp30) outliers start: 20 outliers final: 5 residues processed: 130 average time/residue: 0.2138 time to fit residues: 37.1115 Evaluate side-chains 118 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN C 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132439 restraints weight = 9520.290| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.72 r_work: 0.3397 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7960 Z= 0.241 Angle : 0.628 6.378 10764 Z= 0.346 Chirality : 0.045 0.234 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.953 59.551 1173 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.41 % Favored : 94.14 % Rotamer: Outliers : 4.20 % Allowed : 11.11 % Favored : 84.69 % 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: -0.02 (0.28), residues: 888 helix: 0.89 (0.21), residues: 568 sheet: -0.38 (0.62), residues: 58 loop : -1.89 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.005 0.001 HIS A 196 PHE 0.020 0.001 PHE A 135 TYR 0.029 0.002 TYR C 182 ARG 0.002 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.845 Fit side-chains REVERT: A 177 MET cc_start: 0.7443 (mmt) cc_final: 0.6732 (tpt) REVERT: A 193 CYS cc_start: 0.7664 (t) cc_final: 0.6931 (m) REVERT: A 205 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7523 (tptt) REVERT: A 224 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 371 TRP cc_start: 0.5824 (OUTLIER) cc_final: 0.5263 (m-90) REVERT: A 375 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5682 (mt) REVERT: A 377 ARG cc_start: 0.6724 (ttp-170) cc_final: 0.5810 (tpt90) REVERT: B 134 ASP cc_start: 0.8509 (p0) cc_final: 0.8097 (p0) REVERT: C 89 MET cc_start: 0.7658 (mmt) cc_final: 0.7367 (mtt) REVERT: C 177 MET cc_start: 0.7413 (mmt) cc_final: 0.6713 (tpt) REVERT: C 193 CYS cc_start: 0.7663 (t) cc_final: 0.6957 (m) REVERT: C 205 LYS cc_start: 0.7787 (tmtt) cc_final: 0.6788 (mmtt) REVERT: C 224 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7204 (t80) REVERT: C 273 LYS cc_start: 0.8692 (mttm) cc_final: 0.8419 (mttt) REVERT: C 371 TRP cc_start: 0.5838 (OUTLIER) cc_final: 0.5280 (m-90) REVERT: C 375 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5692 (mt) REVERT: C 377 ARG cc_start: 0.6716 (ttp-170) cc_final: 0.5809 (tpt90) REVERT: D 134 ASP cc_start: 0.8625 (p0) cc_final: 0.8247 (p0) outliers start: 34 outliers final: 11 residues processed: 146 average time/residue: 0.2108 time to fit residues: 41.0738 Evaluate side-chains 134 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN B 47 ASN C 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134947 restraints weight = 9429.659| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.76 r_work: 0.3403 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7960 Z= 0.220 Angle : 0.592 6.572 10764 Z= 0.328 Chirality : 0.044 0.220 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.578 59.847 1173 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.07 % Favored : 94.59 % Rotamer: Outliers : 4.69 % Allowed : 12.35 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 888 helix: 1.08 (0.21), residues: 568 sheet: -0.38 (0.61), residues: 58 loop : -1.84 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 68 HIS 0.005 0.001 HIS C 196 PHE 0.019 0.001 PHE C 135 TYR 0.032 0.001 TYR C 182 ARG 0.002 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.777 Fit side-chains REVERT: A 78 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4465 (mt) REVERT: A 177 MET cc_start: 0.7400 (mmt) cc_final: 0.6752 (tpt) REVERT: A 193 CYS cc_start: 0.7651 (t) cc_final: 0.6898 (m) REVERT: A 205 LYS cc_start: 0.7839 (tmtt) cc_final: 0.7343 (tptt) REVERT: A 224 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 279 TYR cc_start: 0.7719 (m-10) cc_final: 0.7387 (m-10) REVERT: A 371 TRP cc_start: 0.5621 (OUTLIER) cc_final: 0.5199 (m-90) REVERT: A 375 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5661 (mt) REVERT: A 377 ARG cc_start: 0.6672 (ttp80) cc_final: 0.5654 (tpt90) REVERT: B 134 ASP cc_start: 0.8590 (p0) cc_final: 0.8142 (p0) REVERT: C 78 ILE cc_start: 0.4918 (OUTLIER) cc_final: 0.4486 (mt) REVERT: C 89 MET cc_start: 0.7672 (mmt) cc_final: 0.7393 (mtt) REVERT: C 177 MET cc_start: 0.7392 (mmt) cc_final: 0.6744 (tpt) REVERT: C 193 CYS cc_start: 0.7648 (t) cc_final: 0.6931 (m) REVERT: C 224 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 371 TRP cc_start: 0.5679 (OUTLIER) cc_final: 0.5188 (m-90) REVERT: C 375 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5625 (mt) REVERT: C 377 ARG cc_start: 0.6651 (ttp80) cc_final: 0.5647 (tpt90) REVERT: D 134 ASP cc_start: 0.8596 (p0) cc_final: 0.8193 (p0) outliers start: 38 outliers final: 17 residues processed: 145 average time/residue: 0.1971 time to fit residues: 38.8522 Evaluate side-chains 138 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** C 347 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 = 0.3851 r_free = 0.3851 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132517 restraints weight = 9445.300| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.72 r_work: 0.3427 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7960 Z= 0.224 Angle : 0.579 6.308 10764 Z= 0.320 Chirality : 0.044 0.212 1140 Planarity : 0.005 0.052 1298 Dihedral : 10.145 58.181 1173 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 5.19 % Allowed : 13.70 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 888 helix: 1.25 (0.21), residues: 560 sheet: -0.33 (0.61), residues: 58 loop : -1.85 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.006 0.001 HIS A 163 PHE 0.020 0.001 PHE A 135 TYR 0.031 0.001 TYR C 182 ARG 0.003 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.934 Fit side-chains REVERT: A 78 ILE cc_start: 0.4945 (OUTLIER) cc_final: 0.4474 (mt) REVERT: A 171 LYS cc_start: 0.7741 (tppt) cc_final: 0.7488 (tmtt) REVERT: A 177 MET cc_start: 0.7355 (mmt) cc_final: 0.6676 (tpt) REVERT: A 193 CYS cc_start: 0.7712 (t) cc_final: 0.6966 (m) REVERT: A 224 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 371 TRP cc_start: 0.5309 (OUTLIER) cc_final: 0.4979 (m-90) REVERT: A 375 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5519 (mt) REVERT: A 377 ARG cc_start: 0.6470 (ttp80) cc_final: 0.5512 (tpt90) REVERT: B 19 LYS cc_start: 0.7554 (ptpp) cc_final: 0.6692 (pttt) REVERT: B 97 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 108 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8463 (p0) REVERT: B 134 ASP cc_start: 0.8646 (p0) cc_final: 0.8141 (p0) REVERT: C 78 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.4391 (mt) REVERT: C 89 MET cc_start: 0.7683 (mmt) cc_final: 0.7372 (mtt) REVERT: C 171 LYS cc_start: 0.7700 (tppt) cc_final: 0.7429 (tmtt) REVERT: C 177 MET cc_start: 0.7347 (mmt) cc_final: 0.6696 (tpt) REVERT: C 193 CYS cc_start: 0.7651 (t) cc_final: 0.6899 (m) REVERT: C 224 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7253 (t80) REVERT: C 371 TRP cc_start: 0.5241 (OUTLIER) cc_final: 0.4904 (m-90) REVERT: C 375 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5480 (mt) REVERT: C 377 ARG cc_start: 0.6446 (ttp80) cc_final: 0.5499 (tpt90) REVERT: D 19 LYS cc_start: 0.7383 (ptpp) cc_final: 0.6686 (pttt) REVERT: D 97 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: D 134 ASP cc_start: 0.8632 (p0) cc_final: 0.8180 (p0) outliers start: 42 outliers final: 24 residues processed: 141 average time/residue: 0.1896 time to fit residues: 36.7568 Evaluate side-chains 145 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 241 GLN ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134609 restraints weight = 9460.310| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.73 r_work: 0.3408 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 7960 Z= 0.200 Angle : 0.559 6.145 10764 Z= 0.308 Chirality : 0.043 0.197 1140 Planarity : 0.005 0.051 1298 Dihedral : 9.770 57.587 1173 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.39 % Favored : 95.38 % Rotamer: Outliers : 5.43 % Allowed : 14.94 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 888 helix: 1.34 (0.21), residues: 556 sheet: -0.19 (0.61), residues: 58 loop : -2.00 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 68 HIS 0.006 0.001 HIS A 163 PHE 0.018 0.001 PHE A 135 TYR 0.031 0.001 TYR C 182 ARG 0.002 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.846 Fit side-chains REVERT: A 78 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4468 (mt) REVERT: A 123 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7574 (p) REVERT: A 171 LYS cc_start: 0.7652 (tppt) cc_final: 0.7283 (tmtt) REVERT: A 174 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5523 (ptm) REVERT: A 177 MET cc_start: 0.7484 (mmt) cc_final: 0.6830 (tpt) REVERT: A 193 CYS cc_start: 0.7673 (t) cc_final: 0.6946 (m) REVERT: A 201 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: A 224 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 279 TYR cc_start: 0.7622 (m-10) cc_final: 0.7300 (m-10) REVERT: A 371 TRP cc_start: 0.5368 (OUTLIER) cc_final: 0.5073 (m-90) REVERT: A 375 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5698 (mt) REVERT: A 377 ARG cc_start: 0.6507 (ttp80) cc_final: 0.5521 (tpt90) REVERT: B 97 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: B 108 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8469 (p0) REVERT: B 134 ASP cc_start: 0.8653 (p0) cc_final: 0.8148 (p0) REVERT: C 78 ILE cc_start: 0.4889 (OUTLIER) cc_final: 0.4444 (mt) REVERT: C 89 MET cc_start: 0.7623 (mmt) cc_final: 0.7373 (mtt) REVERT: C 123 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7539 (p) REVERT: C 171 LYS cc_start: 0.7570 (tppt) cc_final: 0.7191 (tmtt) REVERT: C 174 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5494 (ptm) REVERT: C 177 MET cc_start: 0.7347 (mmt) cc_final: 0.6714 (tpt) REVERT: C 193 CYS cc_start: 0.7617 (t) cc_final: 0.6889 (m) REVERT: C 201 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 224 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7270 (t80) REVERT: C 279 TYR cc_start: 0.7602 (m-10) cc_final: 0.7230 (m-10) REVERT: C 371 TRP cc_start: 0.5327 (OUTLIER) cc_final: 0.5024 (m-90) REVERT: C 375 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5694 (mt) REVERT: C 377 ARG cc_start: 0.6485 (ttp80) cc_final: 0.5510 (tpt90) REVERT: D 19 LYS cc_start: 0.7385 (ptpp) cc_final: 0.6622 (pttt) REVERT: D 97 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: D 108 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8530 (p0) REVERT: D 134 ASP cc_start: 0.8635 (p0) cc_final: 0.8173 (p0) outliers start: 44 outliers final: 16 residues processed: 139 average time/residue: 0.1941 time to fit residues: 37.1379 Evaluate side-chains 144 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 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 = 0.3843 r_free = 0.3843 target = 0.161419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132117 restraints weight = 9454.687| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.70 r_work: 0.3378 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7960 Z= 0.200 Angle : 0.557 6.187 10764 Z= 0.306 Chirality : 0.043 0.201 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.481 56.522 1173 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 5.19 % Allowed : 15.19 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 888 helix: 1.36 (0.21), residues: 566 sheet: -0.09 (0.62), residues: 58 loop : -1.74 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 68 HIS 0.007 0.001 HIS A 163 PHE 0.017 0.001 PHE A 135 TYR 0.033 0.001 TYR C 182 ARG 0.002 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.857 Fit side-chains REVERT: A 78 ILE cc_start: 0.4917 (OUTLIER) cc_final: 0.4438 (mt) REVERT: A 123 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7496 (p) REVERT: A 171 LYS cc_start: 0.7642 (tppt) cc_final: 0.7350 (tmtt) REVERT: A 177 MET cc_start: 0.7476 (mmt) cc_final: 0.6791 (tpt) REVERT: A 193 CYS cc_start: 0.7816 (t) cc_final: 0.7168 (m) REVERT: A 201 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: A 224 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7218 (t80) REVERT: A 371 TRP cc_start: 0.5238 (OUTLIER) cc_final: 0.4956 (m-90) REVERT: A 375 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5741 (mt) REVERT: A 377 ARG cc_start: 0.6497 (ttp80) cc_final: 0.5454 (tpt90) REVERT: B 97 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 134 ASP cc_start: 0.8596 (p0) cc_final: 0.8073 (p0) REVERT: C 78 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4469 (mt) REVERT: C 89 MET cc_start: 0.7562 (mmt) cc_final: 0.7338 (mtt) REVERT: C 123 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7476 (p) REVERT: C 171 LYS cc_start: 0.7587 (tppt) cc_final: 0.7291 (tmtt) REVERT: C 177 MET cc_start: 0.7451 (mmt) cc_final: 0.6786 (tpt) REVERT: C 193 CYS cc_start: 0.7651 (t) cc_final: 0.6980 (m) REVERT: C 201 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: C 224 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7295 (t80) REVERT: C 279 TYR cc_start: 0.7580 (m-10) cc_final: 0.7232 (m-10) REVERT: C 371 TRP cc_start: 0.5238 (OUTLIER) cc_final: 0.4935 (m-90) REVERT: C 375 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5716 (mt) REVERT: C 377 ARG cc_start: 0.6575 (ttp80) cc_final: 0.5564 (tpt90) REVERT: D 19 LYS cc_start: 0.7444 (ptpp) cc_final: 0.6702 (pttt) REVERT: D 97 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7601 (tt0) outliers start: 42 outliers final: 18 residues processed: 136 average time/residue: 0.1894 time to fit residues: 35.2514 Evaluate side-chains 144 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** C 347 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 = 0.3849 r_free = 0.3849 target = 0.161671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132779 restraints weight = 9543.901| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.70 r_work: 0.3429 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7960 Z= 0.222 Angle : 0.573 6.159 10764 Z= 0.315 Chirality : 0.044 0.213 1140 Planarity : 0.005 0.053 1298 Dihedral : 9.360 56.330 1173 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 3.95 % Allowed : 17.28 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 888 helix: 1.45 (0.21), residues: 556 sheet: 0.01 (0.62), residues: 58 loop : -1.82 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.006 0.001 HIS C 163 PHE 0.017 0.001 PHE A 135 TYR 0.030 0.001 TYR C 182 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.888 Fit side-chains REVERT: A 78 ILE cc_start: 0.4886 (OUTLIER) cc_final: 0.4416 (mt) REVERT: A 171 LYS cc_start: 0.7639 (tppt) cc_final: 0.7338 (tmtt) REVERT: A 177 MET cc_start: 0.7469 (mmt) cc_final: 0.6784 (tpt) REVERT: A 193 CYS cc_start: 0.7776 (t) cc_final: 0.7150 (m) REVERT: A 201 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: A 224 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7244 (t80) REVERT: A 279 TYR cc_start: 0.7573 (m-10) cc_final: 0.7212 (m-10) REVERT: A 371 TRP cc_start: 0.5172 (OUTLIER) cc_final: 0.4890 (m-90) REVERT: A 375 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5679 (mt) REVERT: A 377 ARG cc_start: 0.6371 (ttp80) cc_final: 0.5333 (tpt90) REVERT: B 97 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: C 78 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4447 (mt) REVERT: C 89 MET cc_start: 0.7553 (mmt) cc_final: 0.7311 (mtt) REVERT: C 171 LYS cc_start: 0.7561 (tppt) cc_final: 0.7257 (tmtt) REVERT: C 177 MET cc_start: 0.7442 (mmt) cc_final: 0.6765 (tpt) REVERT: C 193 CYS cc_start: 0.7643 (t) cc_final: 0.7012 (m) REVERT: C 201 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: C 224 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7269 (t80) REVERT: C 371 TRP cc_start: 0.5177 (OUTLIER) cc_final: 0.4884 (m-90) REVERT: C 375 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5673 (mt) REVERT: C 377 ARG cc_start: 0.6364 (ttp80) cc_final: 0.5332 (tpt90) REVERT: D 19 LYS cc_start: 0.7284 (ptpp) cc_final: 0.6550 (pttt) REVERT: D 97 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: D 136 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8209 (tp30) outliers start: 32 outliers final: 17 residues processed: 130 average time/residue: 0.2015 time to fit residues: 35.7713 Evaluate side-chains 139 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** C 347 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 = 0.3860 r_free = 0.3860 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134456 restraints weight = 9577.051| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.66 r_work: 0.3382 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7960 Z= 0.199 Angle : 0.559 6.115 10764 Z= 0.308 Chirality : 0.043 0.200 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.180 56.591 1173 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 3.95 % Allowed : 17.16 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 888 helix: 1.48 (0.21), residues: 556 sheet: 0.14 (0.62), residues: 58 loop : -1.69 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.007 0.001 HIS A 163 PHE 0.018 0.001 PHE C 135 TYR 0.027 0.001 TYR A 182 ARG 0.002 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.818 Fit side-chains REVERT: A 78 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4470 (mt) REVERT: A 171 LYS cc_start: 0.7657 (tppt) cc_final: 0.7353 (tmtt) REVERT: A 177 MET cc_start: 0.7387 (mmt) cc_final: 0.6804 (tpt) REVERT: A 193 CYS cc_start: 0.7709 (t) cc_final: 0.7119 (m) REVERT: A 201 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: A 224 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 279 TYR cc_start: 0.7593 (m-10) cc_final: 0.7248 (m-10) REVERT: A 371 TRP cc_start: 0.5207 (OUTLIER) cc_final: 0.4957 (m-90) REVERT: A 375 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5734 (mt) REVERT: A 377 ARG cc_start: 0.6418 (ttp80) cc_final: 0.5365 (tpt90) REVERT: B 97 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: C 78 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4492 (mt) REVERT: C 89 MET cc_start: 0.7480 (mmt) cc_final: 0.7262 (mtt) REVERT: C 171 LYS cc_start: 0.7596 (tppt) cc_final: 0.7291 (tmtt) REVERT: C 177 MET cc_start: 0.7344 (mmt) cc_final: 0.6772 (tpt) REVERT: C 193 CYS cc_start: 0.7649 (t) cc_final: 0.7047 (m) REVERT: C 201 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: C 224 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7268 (t80) REVERT: C 279 TYR cc_start: 0.7570 (m-10) cc_final: 0.7218 (m-10) REVERT: C 371 TRP cc_start: 0.5224 (OUTLIER) cc_final: 0.4976 (m-90) REVERT: C 375 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5735 (mt) REVERT: C 377 ARG cc_start: 0.6404 (ttp80) cc_final: 0.5371 (tpt90) REVERT: D 19 LYS cc_start: 0.7255 (ptpp) cc_final: 0.6508 (pttt) REVERT: D 97 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: D 136 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8090 (tp30) outliers start: 32 outliers final: 18 residues processed: 124 average time/residue: 0.2088 time to fit residues: 34.8089 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.0020 chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 HIS ** C 347 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 = 0.3862 r_free = 0.3862 target = 0.162858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134277 restraints weight = 9617.188| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.68 r_work: 0.3430 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7960 Z= 0.200 Angle : 0.561 6.174 10764 Z= 0.308 Chirality : 0.043 0.201 1140 Planarity : 0.005 0.052 1298 Dihedral : 8.936 56.600 1173 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 3.83 % Allowed : 16.91 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 888 helix: 1.51 (0.21), residues: 558 sheet: 0.23 (0.63), residues: 58 loop : -1.87 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 68 HIS 0.007 0.001 HIS C 163 PHE 0.017 0.001 PHE A 135 TYR 0.024 0.001 TYR A 182 ARG 0.002 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.831 Fit side-chains REVERT: A 78 ILE cc_start: 0.4964 (OUTLIER) cc_final: 0.4479 (mt) REVERT: A 171 LYS cc_start: 0.7680 (tppt) cc_final: 0.7377 (tmtt) REVERT: A 177 MET cc_start: 0.7369 (mmt) cc_final: 0.6771 (tpt) REVERT: A 193 CYS cc_start: 0.7757 (t) cc_final: 0.7178 (m) REVERT: A 201 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: A 224 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 279 TYR cc_start: 0.7573 (m-10) cc_final: 0.7229 (m-10) REVERT: A 371 TRP cc_start: 0.5217 (OUTLIER) cc_final: 0.4965 (m-90) REVERT: A 375 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5735 (mt) REVERT: A 377 ARG cc_start: 0.6320 (ttp80) cc_final: 0.5294 (tpt90) REVERT: B 97 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 78 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4450 (mt) REVERT: C 89 MET cc_start: 0.7538 (mmt) cc_final: 0.7277 (mtt) REVERT: C 171 LYS cc_start: 0.7620 (tppt) cc_final: 0.7327 (tmtt) REVERT: C 177 MET cc_start: 0.7364 (mmt) cc_final: 0.6778 (tpt) REVERT: C 193 CYS cc_start: 0.7741 (t) cc_final: 0.7187 (m) REVERT: C 201 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: C 224 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7274 (t80) REVERT: C 279 TYR cc_start: 0.7579 (m-10) cc_final: 0.7213 (m-10) REVERT: C 371 TRP cc_start: 0.5249 (OUTLIER) cc_final: 0.4998 (m-90) REVERT: C 375 ILE cc_start: 0.6024 (OUTLIER) cc_final: 0.5727 (mt) REVERT: C 377 ARG cc_start: 0.6300 (ttp80) cc_final: 0.5291 (tpt90) REVERT: D 19 LYS cc_start: 0.7313 (ptpp) cc_final: 0.6576 (pttt) REVERT: D 97 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7674 (tt0) outliers start: 31 outliers final: 17 residues processed: 124 average time/residue: 0.2129 time to fit residues: 35.3457 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 HIS ** C 347 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 = 0.3857 r_free = 0.3857 target = 0.162309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133798 restraints weight = 9584.352| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.67 r_work: 0.3382 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7960 Z= 0.213 Angle : 0.568 6.149 10764 Z= 0.312 Chirality : 0.043 0.206 1140 Planarity : 0.005 0.052 1298 Dihedral : 8.764 56.655 1170 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 3.58 % Allowed : 17.28 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 888 helix: 1.52 (0.21), residues: 558 sheet: 0.37 (0.64), residues: 58 loop : -1.86 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 68 HIS 0.007 0.001 HIS A 163 PHE 0.017 0.001 PHE C 135 TYR 0.043 0.002 TYR A 182 ARG 0.002 0.000 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.43 seconds wall clock time: 80 minutes 17.50 seconds (4817.50 seconds total)