Starting phenix.real_space_refine on Wed Mar 12 09:43:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2n_38858/03_2025/8y2n_38858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2n_38858/03_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_38858/03_2025/8y2n_38858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2n_38858/03_2025/8y2n_38858.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2n_38858/03_2025/8y2n_38858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2n_38858/03_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-5624/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: 5.61, per 1000 atoms: 0.73 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=4, 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 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 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: 0.69 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: 2.06 Time building geometry restraints manager: 2.26 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: 4002 17.69 - 35.37: 468 35.37 - 53.06: 88 53.06 - 70.75: 38 70.75 - 88.43: 8 Dihedral angle restraints: 4604 sinusoidal: 1934 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 4601 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: 83 2.58 - 3.16: 6758 3.16 - 3.74: 11804 3.74 - 4.32: 16487 4.32 - 4.90: 27540 Nonbonded interactions: 62672 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=" OH TYR A 224 " pdb=" OG SER A 266 " model vdw 2.041 3.040 nonbonded pdb=" OH TYR C 224 " pdb=" OG SER C 266 " model vdw 2.041 3.040 nonbonded pdb=" O LEU A 261 " pdb=" OG SER A 265 " model vdw 2.091 3.040 ... (remaining 62667 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- 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= 0.713 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 : 0.802 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: 0.2434 time to fit residues: 48.7316 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 : 0.844 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.165346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132247 restraints weight = 9496.385| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.21 r_work: 0.3402 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7960 Z= 0.268 Angle : 0.706 8.568 10764 Z= 0.387 Chirality : 0.048 0.256 1140 Planarity : 0.006 0.049 1298 Dihedral : 11.231 60.693 1173 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.53 % Favored : 93.24 % Rotamer: Outliers : 2.47 % Allowed : 9.75 % Favored : 87.78 % 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: -0.25 (0.28), residues: 888 helix: 0.79 (0.22), residues: 560 sheet: -0.35 (0.66), residues: 58 loop : -2.15 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 68 HIS 0.017 0.002 HIS A 163 PHE 0.020 0.002 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 137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.878 Fit side-chains REVERT: A 177 MET cc_start: 0.7332 (mmt) cc_final: 0.6690 (tpt) REVERT: A 193 CYS cc_start: 0.7556 (t) cc_final: 0.7075 (m) REVERT: A 205 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7499 (tptt) REVERT: A 371 TRP cc_start: 0.6029 (OUTLIER) cc_final: 0.5387 (m-90) REVERT: A 375 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5915 (mt) REVERT: A 377 ARG cc_start: 0.6699 (ttp-170) cc_final: 0.5837 (tpt90) REVERT: B 134 ASP cc_start: 0.8585 (p0) cc_final: 0.8311 (p0) REVERT: C 89 MET cc_start: 0.7488 (mmt) cc_final: 0.7284 (mtt) REVERT: C 177 MET cc_start: 0.7315 (mmt) cc_final: 0.6654 (tpt) REVERT: C 193 CYS cc_start: 0.7514 (t) cc_final: 0.7006 (m) REVERT: C 205 LYS cc_start: 0.7726 (tmtt) cc_final: 0.7339 (tptt) REVERT: C 371 TRP cc_start: 0.6024 (OUTLIER) cc_final: 0.5359 (m-90) REVERT: C 375 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.5950 (mt) REVERT: C 377 ARG cc_start: 0.6775 (ttp-170) cc_final: 0.5852 (tpt90) REVERT: D 134 ASP cc_start: 0.8607 (p0) cc_final: 0.8335 (p0) REVERT: D 136 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8011 (tp30) outliers start: 20 outliers final: 4 residues processed: 131 average time/residue: 0.2432 time to fit residues: 42.5186 Evaluate side-chains 118 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.161993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132454 restraints weight = 9551.295| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.75 r_work: 0.3419 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7960 Z= 0.233 Angle : 0.622 6.272 10764 Z= 0.342 Chirality : 0.045 0.231 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.908 59.451 1173 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.18 % Favored : 94.37 % Rotamer: Outliers : 3.70 % Allowed : 11.36 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 888 helix: 0.93 (0.21), residues: 568 sheet: -0.39 (0.63), residues: 58 loop : -1.90 (0.37), 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 0.020 0.001 PHE A 135 TYR 0.031 0.002 TYR C 182 ARG 0.003 0.001 ARG B 25 *********************** 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 155 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.808 Fit side-chains REVERT: A 177 MET cc_start: 0.7486 (mmt) cc_final: 0.6777 (tpt) REVERT: A 193 CYS cc_start: 0.7657 (t) cc_final: 0.7007 (m) REVERT: A 205 LYS cc_start: 0.7890 (tmtt) cc_final: 0.7546 (tptt) REVERT: A 224 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7228 (t80) REVERT: A 371 TRP cc_start: 0.5819 (OUTLIER) cc_final: 0.5263 (m-90) REVERT: A 375 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5690 (mt) REVERT: A 377 ARG cc_start: 0.6774 (ttp80) cc_final: 0.5849 (tpt90) REVERT: B 134 ASP cc_start: 0.8521 (p0) cc_final: 0.8093 (p0) REVERT: C 89 MET cc_start: 0.7632 (mmt) cc_final: 0.7347 (mtt) REVERT: C 177 MET cc_start: 0.7418 (mmt) cc_final: 0.6712 (tpt) REVERT: C 205 LYS cc_start: 0.7799 (tmtt) cc_final: 0.7300 (tptt) REVERT: C 224 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.7242 (t80) REVERT: C 273 LYS cc_start: 0.8690 (mttm) cc_final: 0.8425 (mttt) REVERT: C 371 TRP cc_start: 0.5776 (OUTLIER) cc_final: 0.5230 (m-90) REVERT: C 375 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5704 (mt) REVERT: C 377 ARG cc_start: 0.6722 (ttp80) cc_final: 0.5823 (tpt90) REVERT: D 134 ASP cc_start: 0.8554 (p0) cc_final: 0.8139 (p0) outliers start: 30 outliers final: 12 residues processed: 143 average time/residue: 0.2120 time to fit residues: 40.4642 Evaluate side-chains 134 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 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 338 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133526 restraints weight = 9435.437| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.73 r_work: 0.3390 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7960 Z= 0.214 Angle : 0.590 6.758 10764 Z= 0.327 Chirality : 0.044 0.219 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.527 59.865 1173 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.07 % Favored : 94.59 % Rotamer: Outliers : 4.69 % Allowed : 11.98 % Favored : 83.33 % 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: 0.21 (0.28), residues: 888 helix: 1.10 (0.21), residues: 568 sheet: -0.45 (0.62), residues: 58 loop : -1.85 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 68 HIS 0.005 0.001 HIS A 196 PHE 0.019 0.001 PHE C 135 TYR 0.032 0.001 TYR C 182 ARG 0.002 0.000 ARG A 112 *********************** 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 153 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.812 Fit side-chains REVERT: A 78 ILE cc_start: 0.4969 (OUTLIER) cc_final: 0.4505 (mt) REVERT: A 174 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5598 (ptm) REVERT: A 177 MET cc_start: 0.7394 (mmt) cc_final: 0.6739 (tpt) REVERT: A 193 CYS cc_start: 0.7636 (t) cc_final: 0.6886 (m) REVERT: A 224 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7192 (t80) REVERT: A 371 TRP cc_start: 0.5610 (OUTLIER) cc_final: 0.5188 (m-90) REVERT: A 375 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5669 (mt) REVERT: A 377 ARG cc_start: 0.6678 (ttp80) cc_final: 0.5675 (tpt90) REVERT: B 134 ASP cc_start: 0.8571 (p0) cc_final: 0.8138 (p0) REVERT: C 78 ILE cc_start: 0.4952 (OUTLIER) cc_final: 0.4517 (mt) REVERT: C 89 MET cc_start: 0.7662 (mmt) cc_final: 0.7385 (mtt) REVERT: C 174 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5641 (ptm) REVERT: C 177 MET cc_start: 0.7376 (mmt) cc_final: 0.6731 (tpt) REVERT: C 193 CYS cc_start: 0.7631 (t) cc_final: 0.6908 (m) REVERT: C 224 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7280 (t80) REVERT: C 371 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.5174 (m-90) REVERT: C 375 ILE cc_start: 0.6088 (OUTLIER) cc_final: 0.5649 (mt) REVERT: C 377 ARG cc_start: 0.6720 (ttp80) cc_final: 0.5727 (tpt90) REVERT: D 134 ASP cc_start: 0.8579 (p0) cc_final: 0.8157 (p0) outliers start: 38 outliers final: 15 residues processed: 138 average time/residue: 0.2380 time to fit residues: 45.1952 Evaluate side-chains 136 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 A residue 379 LEU 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 C residue 379 LEU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 136 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131800 restraints weight = 9494.056| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.75 r_work: 0.3408 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7960 Z= 0.217 Angle : 0.575 6.275 10764 Z= 0.317 Chirality : 0.044 0.209 1140 Planarity : 0.005 0.052 1298 Dihedral : 10.130 59.806 1173 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 4.57 % Allowed : 13.46 % Favored : 81.98 % 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: 0.34 (0.28), residues: 888 helix: 1.27 (0.21), residues: 560 sheet: -0.38 (0.62), residues: 58 loop : -1.87 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.005 0.001 HIS C 111 PHE 0.020 0.001 PHE C 135 TYR 0.032 0.001 TYR A 182 ARG 0.002 0.000 ARG A 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 155 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.759 Fit side-chains REVERT: A 78 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4520 (mt) REVERT: A 171 LYS cc_start: 0.7769 (tppt) cc_final: 0.7523 (tmtt) REVERT: A 177 MET cc_start: 0.7405 (mmt) cc_final: 0.6755 (tpt) REVERT: A 193 CYS cc_start: 0.7782 (t) cc_final: 0.7048 (m) REVERT: A 224 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 371 TRP cc_start: 0.5389 (OUTLIER) cc_final: 0.5056 (m-90) REVERT: A 375 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5597 (mt) REVERT: A 377 ARG cc_start: 0.6475 (ttp80) cc_final: 0.5490 (tpt90) REVERT: B 19 LYS cc_start: 0.7615 (ptpp) cc_final: 0.6837 (pttt) REVERT: B 108 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8482 (p0) REVERT: B 134 ASP cc_start: 0.8636 (p0) cc_final: 0.8160 (p0) REVERT: C 78 ILE cc_start: 0.4896 (OUTLIER) cc_final: 0.4446 (mt) REVERT: C 89 MET cc_start: 0.7683 (mmt) cc_final: 0.7390 (mtt) REVERT: C 171 LYS cc_start: 0.7774 (tppt) cc_final: 0.7524 (tmtt) REVERT: C 177 MET cc_start: 0.7378 (mmt) cc_final: 0.6739 (tpt) REVERT: C 193 CYS cc_start: 0.7644 (t) cc_final: 0.6901 (m) REVERT: C 224 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7292 (t80) REVERT: C 279 TYR cc_start: 0.7624 (m-10) cc_final: 0.7266 (m-10) REVERT: C 371 TRP cc_start: 0.5382 (OUTLIER) cc_final: 0.5044 (m-90) REVERT: C 375 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5568 (mt) REVERT: C 377 ARG cc_start: 0.6468 (ttp80) cc_final: 0.5499 (tpt90) REVERT: D 19 LYS cc_start: 0.7431 (ptpp) cc_final: 0.6731 (pttt) REVERT: D 97 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 108 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8526 (p0) REVERT: D 134 ASP cc_start: 0.8664 (p0) cc_final: 0.8203 (p0) outliers start: 37 outliers final: 17 residues processed: 138 average time/residue: 0.2065 time to fit residues: 39.5439 Evaluate side-chains 138 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 A residue 379 LEU Chi-restraints excluded: chain B residue 108 ASN 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 97 GLU Chi-restraints excluded: chain D residue 108 ASN 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: 0.2980 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 256 HIS C 241 GLN ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132696 restraints weight = 9477.626| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.71 r_work: 0.3427 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7960 Z= 0.232 Angle : 0.572 6.175 10764 Z= 0.315 Chirality : 0.044 0.210 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.846 57.545 1173 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 5.31 % Allowed : 14.07 % Favored : 80.62 % 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: 0.33 (0.28), residues: 888 helix: 1.31 (0.21), residues: 556 sheet: -0.19 (0.62), residues: 58 loop : -2.01 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.007 0.001 HIS C 163 PHE 0.019 0.001 PHE A 135 TYR 0.032 0.001 TYR C 182 ARG 0.002 0.000 ARG B 78 *********************** 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 161 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.736 Fit side-chains REVERT: A 78 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4441 (mt) REVERT: A 123 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 171 LYS cc_start: 0.7640 (tppt) cc_final: 0.7357 (tmtt) REVERT: A 177 MET cc_start: 0.7388 (mmt) cc_final: 0.6716 (tpt) REVERT: A 193 CYS cc_start: 0.7712 (t) cc_final: 0.6991 (m) REVERT: A 201 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: A 224 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 279 TYR cc_start: 0.7637 (m-10) cc_final: 0.7275 (m-10) REVERT: A 371 TRP cc_start: 0.5295 (OUTLIER) cc_final: 0.4988 (m-90) REVERT: A 375 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5660 (mt) REVERT: A 377 ARG cc_start: 0.6456 (ttp80) cc_final: 0.5478 (tpt90) REVERT: B 108 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8546 (p0) REVERT: B 134 ASP cc_start: 0.8645 (p0) cc_final: 0.8142 (p0) REVERT: C 78 ILE cc_start: 0.4872 (OUTLIER) cc_final: 0.4424 (mt) REVERT: C 89 MET cc_start: 0.7648 (mmt) cc_final: 0.7395 (mtt) REVERT: C 123 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 171 LYS cc_start: 0.7644 (tppt) cc_final: 0.7365 (tmtt) REVERT: C 177 MET cc_start: 0.7350 (mmt) cc_final: 0.6716 (tpt) REVERT: C 193 CYS cc_start: 0.7624 (t) cc_final: 0.6912 (m) REVERT: C 201 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: C 224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7288 (t80) REVERT: C 371 TRP cc_start: 0.5284 (OUTLIER) cc_final: 0.4962 (m-90) REVERT: C 375 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5663 (mt) REVERT: C 377 ARG cc_start: 0.6503 (ttp80) cc_final: 0.5541 (tpt90) REVERT: D 19 LYS cc_start: 0.7324 (ptpp) cc_final: 0.6585 (pttt) REVERT: D 97 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: D 108 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8517 (p0) outliers start: 43 outliers final: 20 residues processed: 143 average time/residue: 0.1754 time to fit residues: 34.5981 Evaluate side-chains 147 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 VAL 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 108 ASN Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 133 THR 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 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 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: 10.0000 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132044 restraints weight = 9410.641| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.67 r_work: 0.3397 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7960 Z= 0.236 Angle : 0.571 6.206 10764 Z= 0.314 Chirality : 0.044 0.218 1140 Planarity : 0.005 0.053 1298 Dihedral : 9.645 56.988 1173 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.84 % Favored : 94.93 % Rotamer: Outliers : 5.43 % Allowed : 14.69 % Favored : 79.88 % 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: 0.39 (0.28), residues: 888 helix: 1.35 (0.21), residues: 556 sheet: -0.09 (0.62), residues: 58 loop : -1.97 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.007 0.001 HIS C 163 PHE 0.017 0.001 PHE A 135 TYR 0.033 0.002 TYR C 182 ARG 0.002 0.000 ARG B 78 *********************** 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 152 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.102 Fit side-chains REVERT: A 78 ILE cc_start: 0.5014 (OUTLIER) cc_final: 0.4509 (mt) REVERT: A 171 LYS cc_start: 0.7680 (tppt) cc_final: 0.7382 (tmtt) REVERT: A 177 MET cc_start: 0.7521 (mmt) cc_final: 0.6865 (tpt) REVERT: A 193 CYS cc_start: 0.7808 (t) cc_final: 0.7185 (m) REVERT: A 201 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: A 224 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 371 TRP cc_start: 0.5311 (OUTLIER) cc_final: 0.5012 (m-90) REVERT: A 375 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5744 (mt) REVERT: A 377 ARG cc_start: 0.6467 (ttp80) cc_final: 0.5435 (tpt90) REVERT: C 78 ILE cc_start: 0.4966 (OUTLIER) cc_final: 0.4493 (mt) REVERT: C 89 MET cc_start: 0.7541 (mmt) cc_final: 0.7320 (mtt) REVERT: C 171 LYS cc_start: 0.7674 (tppt) cc_final: 0.7380 (tmtt) REVERT: C 177 MET cc_start: 0.7507 (mmt) cc_final: 0.6857 (tpt) REVERT: C 193 CYS cc_start: 0.7722 (t) cc_final: 0.7126 (m) REVERT: C 201 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: C 224 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 371 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.4957 (m-90) REVERT: C 375 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5698 (mt) REVERT: C 377 ARG cc_start: 0.6532 (ttp80) cc_final: 0.5517 (tpt90) REVERT: D 97 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: D 108 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8538 (p0) REVERT: D 140 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7903 (mm-30) outliers start: 44 outliers final: 22 residues processed: 138 average time/residue: 0.2388 time to fit residues: 45.8905 Evaluate side-chains 140 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 162 LEU 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 241 GLN 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 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 185 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 241 GLN 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 97 GLU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 THR 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: 0.7980 chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 256 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131072 restraints weight = 9594.788| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.80 r_work: 0.3403 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3248 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= 0.188 Angle : 0.555 6.111 10764 Z= 0.307 Chirality : 0.043 0.199 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.452 56.781 1173 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 4.69 % Allowed : 15.93 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 888 helix: 1.40 (0.21), residues: 556 sheet: -0.02 (0.63), residues: 58 loop : -1.91 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.007 0.001 HIS C 163 PHE 0.018 0.001 PHE A 135 TYR 0.035 0.001 TYR C 182 ARG 0.002 0.000 ARG C 112 *********************** 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 143 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.799 Fit side-chains REVERT: A 78 ILE cc_start: 0.4802 (OUTLIER) cc_final: 0.4350 (mt) REVERT: A 171 LYS cc_start: 0.7588 (tppt) cc_final: 0.7295 (tmtt) REVERT: A 177 MET cc_start: 0.7441 (mmt) cc_final: 0.6750 (tpt) REVERT: A 193 CYS cc_start: 0.7744 (t) cc_final: 0.7104 (m) REVERT: A 201 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 224 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7251 (t80) REVERT: A 371 TRP cc_start: 0.5155 (OUTLIER) cc_final: 0.4876 (m-90) REVERT: A 375 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5615 (mt) REVERT: A 377 ARG cc_start: 0.6404 (ttp80) cc_final: 0.5349 (tpt90) REVERT: C 78 ILE cc_start: 0.4833 (OUTLIER) cc_final: 0.4390 (mt) REVERT: C 89 MET cc_start: 0.7575 (mmt) cc_final: 0.7309 (mtt) REVERT: C 171 LYS cc_start: 0.7595 (tppt) cc_final: 0.7299 (tmtt) REVERT: C 177 MET cc_start: 0.7429 (mmt) cc_final: 0.6743 (tpt) REVERT: C 193 CYS cc_start: 0.7629 (t) cc_final: 0.6991 (m) REVERT: C 201 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: C 224 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7254 (t80) REVERT: C 279 TYR cc_start: 0.7584 (m-10) cc_final: 0.7216 (m-10) REVERT: C 371 TRP cc_start: 0.5113 (OUTLIER) cc_final: 0.4829 (m-90) REVERT: C 375 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5629 (mt) REVERT: C 377 ARG cc_start: 0.6464 (ttp80) cc_final: 0.5426 (tpt90) REVERT: D 97 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: D 108 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8513 (p0) REVERT: D 136 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: D 140 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7882 (mm-30) outliers start: 38 outliers final: 19 residues processed: 128 average time/residue: 0.2003 time to fit residues: 35.0288 Evaluate side-chains 137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 162 LEU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3896 r_free = 0.3896 target = 0.166368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138267 restraints weight = 9600.316| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.68 r_work: 0.3495 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7960 Z= 0.150 Angle : 0.528 6.147 10764 Z= 0.292 Chirality : 0.042 0.169 1140 Planarity : 0.005 0.051 1298 Dihedral : 8.896 58.441 1173 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 3.46 % Allowed : 16.91 % 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: 0.76 (0.28), residues: 888 helix: 1.53 (0.21), residues: 560 sheet: 0.19 (0.63), residues: 58 loop : -1.65 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.007 0.001 HIS C 163 PHE 0.020 0.001 PHE A 135 TYR 0.016 0.001 TYR A 139 ARG 0.003 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 144 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.934 Fit side-chains REVERT: A 78 ILE cc_start: 0.4992 (OUTLIER) cc_final: 0.4504 (mt) REVERT: A 171 LYS cc_start: 0.7753 (tppt) cc_final: 0.7482 (tmtt) REVERT: A 177 MET cc_start: 0.7491 (mmt) cc_final: 0.6899 (tpt) REVERT: A 193 CYS cc_start: 0.7761 (t) cc_final: 0.7135 (m) REVERT: A 224 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7252 (t80) REVERT: A 279 TYR cc_start: 0.7457 (m-10) cc_final: 0.7181 (m-10) REVERT: A 371 TRP cc_start: 0.5296 (OUTLIER) cc_final: 0.5082 (m-90) REVERT: A 375 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5827 (mt) REVERT: A 377 ARG cc_start: 0.6543 (ttp80) cc_final: 0.5515 (tpt90) REVERT: C 78 ILE cc_start: 0.4974 (OUTLIER) cc_final: 0.4500 (mt) REVERT: C 89 MET cc_start: 0.7559 (mmt) cc_final: 0.7287 (mtt) REVERT: C 171 LYS cc_start: 0.7761 (tppt) cc_final: 0.7489 (tmtt) REVERT: C 177 MET cc_start: 0.7472 (mmt) cc_final: 0.6884 (tpt) REVERT: C 193 CYS cc_start: 0.7672 (t) cc_final: 0.7008 (m) REVERT: C 224 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7265 (t80) REVERT: C 279 TYR cc_start: 0.7465 (m-10) cc_final: 0.7175 (m-10) REVERT: C 371 TRP cc_start: 0.5239 (OUTLIER) cc_final: 0.5015 (m-90) REVERT: C 375 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5842 (mt) REVERT: C 377 ARG cc_start: 0.6549 (ttp80) cc_final: 0.5530 (tpt90) outliers start: 28 outliers final: 15 residues processed: 134 average time/residue: 0.1925 time to fit residues: 35.6372 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 224 TYR 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 131 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 LEU 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 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135501 restraints weight = 9594.204| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.69 r_work: 0.3416 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3574 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= 0.223 Angle : 0.566 6.284 10764 Z= 0.310 Chirality : 0.044 0.209 1140 Planarity : 0.005 0.052 1298 Dihedral : 8.876 56.512 1170 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 2.59 % Allowed : 18.02 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 888 helix: 1.53 (0.21), residues: 560 sheet: 0.30 (0.65), residues: 58 loop : -1.65 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 371 HIS 0.008 0.001 HIS C 163 PHE 0.016 0.001 PHE C 135 TYR 0.019 0.001 TYR A 139 ARG 0.002 0.000 ARG D 78 ********************** 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 128 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.789 Fit side-chains REVERT: A 78 ILE cc_start: 0.4981 (OUTLIER) cc_final: 0.4484 (mt) REVERT: A 171 LYS cc_start: 0.7633 (tppt) cc_final: 0.7324 (tmtt) REVERT: A 177 MET cc_start: 0.7502 (mmt) cc_final: 0.6930 (tpt) REVERT: A 193 CYS cc_start: 0.7868 (t) cc_final: 0.7276 (m) REVERT: A 224 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.7326 (t80) REVERT: A 279 TYR cc_start: 0.7601 (m-10) cc_final: 0.7235 (m-10) REVERT: A 371 TRP cc_start: 0.5294 (OUTLIER) cc_final: 0.5049 (m-90) REVERT: A 375 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5758 (mt) REVERT: A 377 ARG cc_start: 0.6412 (ttp80) cc_final: 0.5362 (tpt90) REVERT: C 78 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.4483 (mt) REVERT: C 89 MET cc_start: 0.7534 (mmt) cc_final: 0.7283 (mtt) REVERT: C 171 LYS cc_start: 0.7626 (tppt) cc_final: 0.7317 (tmtt) REVERT: C 177 MET cc_start: 0.7479 (mmt) cc_final: 0.6913 (tpt) REVERT: C 193 CYS cc_start: 0.7747 (t) cc_final: 0.7159 (m) REVERT: C 224 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7333 (t80) REVERT: C 279 TYR cc_start: 0.7591 (m-10) cc_final: 0.7247 (m-10) REVERT: C 336 GLU cc_start: 0.7827 (tp30) cc_final: 0.7590 (tp30) REVERT: C 371 TRP cc_start: 0.5256 (OUTLIER) cc_final: 0.4993 (m-90) REVERT: C 375 ILE cc_start: 0.6049 (OUTLIER) cc_final: 0.5748 (mt) REVERT: C 377 ARG cc_start: 0.6406 (ttp80) cc_final: 0.5368 (tpt90) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.1920 time to fit residues: 32.1828 Evaluate side-chains 128 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 224 TYR 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 131 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 LEU 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 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: 0.5980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.162912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134516 restraints weight = 9625.018| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.69 r_work: 0.3454 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7960 Z= 0.204 Angle : 0.556 6.135 10764 Z= 0.305 Chirality : 0.043 0.203 1140 Planarity : 0.005 0.052 1298 Dihedral : 8.798 56.401 1170 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.16 % Rotamer: Outliers : 3.21 % Allowed : 17.41 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 888 helix: 1.53 (0.21), residues: 558 sheet: 0.46 (0.65), residues: 58 loop : -1.71 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.008 0.001 HIS C 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.08 seconds wall clock time: 78 minutes 7.70 seconds (4687.70 seconds total)