Starting phenix.real_space_refine on Sat Dec 28 04:16:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2n_38858/12_2024/8y2n_38858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2n_38858/12_2024/8y2n_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_38858/12_2024/8y2n_38858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2n_38858/12_2024/8y2n_38858.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2n_38858/12_2024/8y2n_38858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2n_38858/12_2024/8y2n_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-5532/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: 5.16, per 1000 atoms: 0.67 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: 1.99 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: 0.65 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: 2.10 Time building geometry restraints manager: 2.25 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.500 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.720 Find NCS groups from input model: 0.240 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- 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 : 0.815 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: 0.2411 time to fit residues: 48.1182 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 : 0.865 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.923 Fit side-chains REVERT: A 177 MET cc_start: 0.6727 (mmt) cc_final: 0.6173 (tpt) REVERT: A 193 CYS cc_start: 0.7174 (t) cc_final: 0.6615 (m) REVERT: A 194 MET cc_start: 0.8240 (ttp) cc_final: 0.8018 (ttp) REVERT: A 371 TRP cc_start: 0.5537 (OUTLIER) cc_final: 0.4948 (m-90) REVERT: A 375 ILE cc_start: 0.5923 (OUTLIER) cc_final: 0.5489 (mt) REVERT: A 377 ARG cc_start: 0.6498 (ttp-170) cc_final: 0.5659 (tpt90) REVERT: B 134 ASP cc_start: 0.8395 (p0) cc_final: 0.8165 (p0) REVERT: C 177 MET cc_start: 0.6718 (mmt) cc_final: 0.6162 (tpt) REVERT: C 193 CYS cc_start: 0.7147 (t) cc_final: 0.6646 (m) REVERT: C 205 LYS cc_start: 0.7534 (tmtt) cc_final: 0.7113 (tptt) REVERT: C 371 TRP cc_start: 0.5545 (OUTLIER) cc_final: 0.4930 (m-90) REVERT: C 375 ILE cc_start: 0.5921 (OUTLIER) cc_final: 0.5484 (mt) REVERT: C 377 ARG cc_start: 0.6572 (ttp-170) cc_final: 0.5684 (tpt90) REVERT: D 134 ASP cc_start: 0.8409 (p0) cc_final: 0.8187 (p0) REVERT: D 136 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7831 (tp30) outliers start: 20 outliers final: 5 residues processed: 130 average time/residue: 0.2347 time to fit residues: 41.1106 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 : 0.896 ------------------------------------------------------------------------------- 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 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7960 Z= 0.224 Angle : 0.618 6.321 10764 Z= 0.340 Chirality : 0.045 0.227 1140 Planarity : 0.005 0.050 1298 Dihedral : 10.883 59.921 1173 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.29 % Favored : 94.26 % Rotamer: Outliers : 4.07 % Allowed : 11.36 % Favored : 84.57 % 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: 0.92 (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 C 196 PHE 0.019 0.001 PHE A 135 TYR 0.029 0.001 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 160 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.804 Fit side-chains REVERT: A 177 MET cc_start: 0.6758 (mmt) cc_final: 0.6241 (tpt) REVERT: A 205 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7354 (tptt) REVERT: A 224 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 293 LYS cc_start: 0.5269 (mtpt) cc_final: 0.5053 (tttm) REVERT: A 371 TRP cc_start: 0.5425 (OUTLIER) cc_final: 0.4971 (m-90) REVERT: A 375 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5358 (mt) REVERT: A 377 ARG cc_start: 0.6549 (ttp-170) cc_final: 0.5683 (tpt90) REVERT: B 134 ASP cc_start: 0.8293 (p0) cc_final: 0.7919 (p0) REVERT: C 177 MET cc_start: 0.6691 (mmt) cc_final: 0.6166 (tpt) REVERT: C 193 CYS cc_start: 0.7276 (t) cc_final: 0.6611 (m) REVERT: C 205 LYS cc_start: 0.7634 (tmtt) cc_final: 0.6691 (mmtt) REVERT: C 224 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6806 (t80) REVERT: C 273 LYS cc_start: 0.8366 (mttm) cc_final: 0.8008 (mttt) REVERT: C 371 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.4998 (m-90) REVERT: C 375 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5385 (mt) REVERT: C 377 ARG cc_start: 0.6546 (ttp-170) cc_final: 0.5688 (tpt90) REVERT: D 134 ASP cc_start: 0.8414 (p0) cc_final: 0.8076 (p0) outliers start: 33 outliers final: 11 residues processed: 147 average time/residue: 0.2129 time to fit residues: 41.9572 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 79 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 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 338 ASN B 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7960 Z= 0.239 Angle : 0.598 6.546 10764 Z= 0.331 Chirality : 0.045 0.228 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.537 59.998 1173 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.41 % Favored : 94.26 % Rotamer: Outliers : 4.44 % Allowed : 12.72 % Favored : 82.84 % 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: 0.18 (0.28), residues: 888 helix: 1.06 (0.21), residues: 568 sheet: -0.36 (0.62), 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 163 PHE 0.020 0.001 PHE A 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 155 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.873 Fit side-chains REVERT: A 78 ILE cc_start: 0.4755 (OUTLIER) cc_final: 0.4331 (mt) REVERT: A 174 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.5063 (ptm) REVERT: A 177 MET cc_start: 0.6627 (mmt) cc_final: 0.6203 (tpt) REVERT: A 193 CYS cc_start: 0.7296 (t) cc_final: 0.6580 (m) REVERT: A 205 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7226 (tptt) REVERT: A 224 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6838 (t80) REVERT: A 371 TRP cc_start: 0.5111 (OUTLIER) cc_final: 0.4768 (m-90) REVERT: A 375 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5343 (mt) REVERT: A 377 ARG cc_start: 0.6564 (ttp80) cc_final: 0.5590 (tpt90) REVERT: B 134 ASP cc_start: 0.8390 (p0) cc_final: 0.7972 (p0) REVERT: C 78 ILE cc_start: 0.4717 (OUTLIER) cc_final: 0.4321 (mt) REVERT: C 171 LYS cc_start: 0.7580 (tppt) cc_final: 0.7244 (tmtt) REVERT: C 174 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5034 (ptm) REVERT: C 177 MET cc_start: 0.6639 (mmt) cc_final: 0.6199 (tpt) REVERT: C 193 CYS cc_start: 0.7281 (t) cc_final: 0.6607 (m) REVERT: C 224 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.6836 (t80) REVERT: C 371 TRP cc_start: 0.5250 (OUTLIER) cc_final: 0.4910 (m-90) REVERT: C 375 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5334 (mt) REVERT: C 377 ARG cc_start: 0.6545 (ttp80) cc_final: 0.5579 (tpt90) REVERT: D 134 ASP cc_start: 0.8385 (p0) cc_final: 0.8012 (p0) outliers start: 36 outliers final: 11 residues processed: 139 average time/residue: 0.2046 time to fit residues: 38.7016 Evaluate side-chains 138 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 78 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS C 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7960 Z= 0.328 Angle : 0.636 6.682 10764 Z= 0.350 Chirality : 0.047 0.247 1140 Planarity : 0.005 0.053 1298 Dihedral : 10.529 58.359 1173 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 5.19 % Allowed : 14.20 % 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: 0.11 (0.27), residues: 888 helix: 1.15 (0.21), residues: 550 sheet: -0.35 (0.62), residues: 58 loop : -2.02 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 371 HIS 0.006 0.002 HIS C 111 PHE 0.021 0.002 PHE C 333 TYR 0.034 0.002 TYR C 182 ARG 0.003 0.001 ARG B 78 *********************** 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 : 0.894 Fit side-chains REVERT: A 78 ILE cc_start: 0.4796 (OUTLIER) cc_final: 0.4353 (mt) REVERT: A 171 LYS cc_start: 0.7526 (tppt) cc_final: 0.7233 (tmtt) REVERT: A 177 MET cc_start: 0.6624 (mmt) cc_final: 0.6195 (tpt) REVERT: A 193 CYS cc_start: 0.7479 (t) cc_final: 0.6835 (m) REVERT: A 205 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7311 (tptt) REVERT: A 224 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.6845 (t80) REVERT: A 279 TYR cc_start: 0.7422 (m-10) cc_final: 0.7019 (m-10) REVERT: A 371 TRP cc_start: 0.5096 (OUTLIER) cc_final: 0.4829 (m-90) REVERT: A 375 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5293 (mt) REVERT: A 377 ARG cc_start: 0.6509 (ttp80) cc_final: 0.5593 (tpt90) REVERT: B 19 LYS cc_start: 0.7656 (ptpp) cc_final: 0.6641 (pttt) REVERT: C 78 ILE cc_start: 0.4761 (OUTLIER) cc_final: 0.4342 (mt) REVERT: C 171 LYS cc_start: 0.7471 (tppt) cc_final: 0.7162 (tmtt) REVERT: C 177 MET cc_start: 0.6639 (mmt) cc_final: 0.6208 (tpt) REVERT: C 193 CYS cc_start: 0.7440 (t) cc_final: 0.6818 (m) REVERT: C 205 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7297 (tptt) REVERT: C 224 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.6838 (t80) REVERT: C 279 TYR cc_start: 0.7425 (m-10) cc_final: 0.7023 (m-10) REVERT: C 371 TRP cc_start: 0.5037 (OUTLIER) cc_final: 0.4768 (m-90) REVERT: C 375 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5306 (mt) REVERT: C 377 ARG cc_start: 0.6502 (ttp80) cc_final: 0.5606 (tpt90) REVERT: D 19 LYS cc_start: 0.7621 (ptpp) cc_final: 0.6827 (pttt) outliers start: 42 outliers final: 25 residues processed: 143 average time/residue: 0.2177 time to fit residues: 42.5029 Evaluate side-chains 147 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 180 ILE Chi-restraints excluded: chain A residue 185 VAL 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 180 ILE 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 Chi-restraints excluded: chain D residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 7960 Z= 0.213 Angle : 0.569 6.113 10764 Z= 0.315 Chirality : 0.043 0.200 1140 Planarity : 0.005 0.051 1298 Dihedral : 9.949 57.723 1173 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.39 % Favored : 95.38 % Rotamer: Outliers : 5.68 % Allowed : 14.57 % Favored : 79.75 % 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: 0.28 (0.28), residues: 888 helix: 1.27 (0.21), residues: 556 sheet: -0.17 (0.62), residues: 58 loop : -2.04 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.006 0.001 HIS A 163 PHE 0.020 0.001 PHE C 135 TYR 0.035 0.001 TYR A 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 165 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.832 Fit side-chains REVERT: A 78 ILE cc_start: 0.4810 (OUTLIER) cc_final: 0.4373 (mt) REVERT: A 171 LYS cc_start: 0.7479 (tppt) cc_final: 0.7088 (tmtt) REVERT: A 174 MET cc_start: 0.5302 (ptt) cc_final: 0.5027 (ptm) REVERT: A 177 MET cc_start: 0.6596 (mmt) cc_final: 0.6164 (tpt) REVERT: A 193 CYS cc_start: 0.7373 (t) cc_final: 0.6792 (m) REVERT: A 224 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.6884 (t80) REVERT: A 371 TRP cc_start: 0.5004 (OUTLIER) cc_final: 0.4800 (m-90) REVERT: A 375 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5272 (mt) REVERT: A 377 ARG cc_start: 0.6457 (ttp80) cc_final: 0.5468 (tpt90) REVERT: B 19 LYS cc_start: 0.7562 (ptpp) cc_final: 0.6778 (pttt) REVERT: B 97 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: C 78 ILE cc_start: 0.4694 (OUTLIER) cc_final: 0.4287 (mt) REVERT: C 171 LYS cc_start: 0.7399 (tppt) cc_final: 0.7099 (tmtt) REVERT: C 177 MET cc_start: 0.6596 (mmt) cc_final: 0.6163 (tpt) REVERT: C 193 CYS cc_start: 0.7252 (t) cc_final: 0.6682 (m) REVERT: C 224 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.6866 (t80) REVERT: C 371 TRP cc_start: 0.4974 (OUTLIER) cc_final: 0.4757 (m-90) REVERT: C 375 ILE cc_start: 0.5670 (OUTLIER) cc_final: 0.5271 (mt) REVERT: C 377 ARG cc_start: 0.6491 (ttp80) cc_final: 0.5522 (tpt90) REVERT: D 19 LYS cc_start: 0.7572 (ptpp) cc_final: 0.6761 (pttt) REVERT: D 97 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7363 (tt0) outliers start: 46 outliers final: 27 residues processed: 145 average time/residue: 0.1995 time to fit residues: 39.8374 Evaluate side-chains 145 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 210 THR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 273 LYS 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 133 THR 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 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 256 HIS ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 7960 Z= 0.218 Angle : 0.569 6.269 10764 Z= 0.314 Chirality : 0.043 0.202 1140 Planarity : 0.005 0.051 1298 Dihedral : 9.590 57.003 1173 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.52 % Favored : 94.26 % Rotamer: Outliers : 5.68 % Allowed : 15.68 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 888 helix: 1.39 (0.21), residues: 556 sheet: -0.07 (0.63), residues: 58 loop : -2.00 (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 C 135 TYR 0.035 0.001 TYR C 182 ARG 0.002 0.000 ARG C 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 153 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.986 Fit side-chains REVERT: A 78 ILE cc_start: 0.4709 (OUTLIER) cc_final: 0.4270 (mt) REVERT: A 171 LYS cc_start: 0.7465 (tppt) cc_final: 0.7165 (tmtt) REVERT: A 177 MET cc_start: 0.6689 (mmt) cc_final: 0.6239 (tpt) REVERT: A 193 CYS cc_start: 0.7272 (t) cc_final: 0.6681 (m) REVERT: A 224 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6867 (t80) REVERT: A 279 TYR cc_start: 0.7192 (m-10) cc_final: 0.6822 (m-10) REVERT: A 375 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5435 (mt) REVERT: A 377 ARG cc_start: 0.6327 (ttp80) cc_final: 0.5317 (tpt90) REVERT: B 97 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: B 108 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8389 (p0) REVERT: C 78 ILE cc_start: 0.4712 (OUTLIER) cc_final: 0.4291 (mt) REVERT: C 171 LYS cc_start: 0.7402 (tppt) cc_final: 0.7095 (tmtt) REVERT: C 177 MET cc_start: 0.6690 (mmt) cc_final: 0.6238 (tpt) REVERT: C 193 CYS cc_start: 0.7262 (t) cc_final: 0.6681 (m) REVERT: C 224 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.6847 (t80) REVERT: C 279 TYR cc_start: 0.7214 (m-10) cc_final: 0.6850 (m-10) REVERT: C 375 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5273 (mt) REVERT: C 377 ARG cc_start: 0.6316 (ttp80) cc_final: 0.5321 (tpt90) REVERT: D 97 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7310 (tt0) outliers start: 46 outliers final: 25 residues processed: 139 average time/residue: 0.2070 time to fit residues: 40.0083 Evaluate side-chains 141 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 41 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 7960 Z= 0.189 Angle : 0.562 6.579 10764 Z= 0.310 Chirality : 0.043 0.190 1140 Planarity : 0.005 0.051 1298 Dihedral : 9.073 56.938 1169 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.16 % Rotamer: Outliers : 4.81 % Allowed : 17.04 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 888 helix: 1.40 (0.21), residues: 556 sheet: 0.05 (0.63), residues: 58 loop : -1.89 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 371 HIS 0.007 0.001 HIS A 163 PHE 0.018 0.001 PHE A 135 TYR 0.034 0.001 TYR C 182 ARG 0.002 0.000 ARG A 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 144 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.095 Fit side-chains REVERT: A 78 ILE cc_start: 0.4705 (OUTLIER) cc_final: 0.4272 (mt) REVERT: A 171 LYS cc_start: 0.7446 (tppt) cc_final: 0.7146 (tmtt) REVERT: A 177 MET cc_start: 0.6668 (mmt) cc_final: 0.6213 (tpt) REVERT: A 193 CYS cc_start: 0.7268 (t) cc_final: 0.6664 (m) REVERT: A 224 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.6792 (t80) REVERT: A 279 TYR cc_start: 0.7215 (m-10) cc_final: 0.6802 (m-10) REVERT: A 371 TRP cc_start: 0.6029 (m-90) cc_final: 0.5507 (m-90) REVERT: A 375 ILE cc_start: 0.5740 (OUTLIER) cc_final: 0.5411 (mt) REVERT: A 377 ARG cc_start: 0.6350 (ttp80) cc_final: 0.5332 (tpt90) REVERT: B 97 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: C 78 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4297 (mt) REVERT: C 171 LYS cc_start: 0.7389 (tppt) cc_final: 0.7078 (tmtt) REVERT: C 177 MET cc_start: 0.6674 (mmt) cc_final: 0.6213 (tpt) REVERT: C 193 CYS cc_start: 0.7245 (t) cc_final: 0.6679 (m) REVERT: C 224 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.6791 (t80) REVERT: C 279 TYR cc_start: 0.7217 (m-10) cc_final: 0.6806 (m-10) REVERT: C 371 TRP cc_start: 0.6069 (m-90) cc_final: 0.5566 (m-90) REVERT: C 375 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5436 (mt) REVERT: C 377 ARG cc_start: 0.6341 (ttp80) cc_final: 0.5335 (tpt90) REVERT: D 97 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7375 (tt0) outliers start: 39 outliers final: 20 residues processed: 130 average time/residue: 0.1966 time to fit residues: 34.8572 Evaluate side-chains 130 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 185 VAL 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 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 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 224 TYR Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU 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 79 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7960 Z= 0.253 Angle : 0.582 6.522 10764 Z= 0.321 Chirality : 0.044 0.217 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.060 56.568 1169 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.18 % Favored : 94.59 % Rotamer: Outliers : 4.81 % Allowed : 16.67 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 888 helix: 1.38 (0.21), residues: 556 sheet: 0.04 (0.63), residues: 58 loop : -1.75 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 371 HIS 0.008 0.001 HIS A 163 PHE 0.017 0.001 PHE A 135 TYR 0.032 0.002 TYR A 182 ARG 0.002 0.000 ARG B 78 *********************** 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 139 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.838 Fit side-chains REVERT: A 78 ILE cc_start: 0.4725 (OUTLIER) cc_final: 0.4285 (mt) REVERT: A 171 LYS cc_start: 0.7455 (tppt) cc_final: 0.7156 (tmtt) REVERT: A 177 MET cc_start: 0.6717 (mmt) cc_final: 0.6260 (tpt) REVERT: A 193 CYS cc_start: 0.7331 (t) cc_final: 0.6798 (m) REVERT: A 224 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.6839 (t80) REVERT: A 279 TYR cc_start: 0.7290 (m-10) cc_final: 0.6898 (m-10) REVERT: A 375 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5432 (mt) REVERT: B 97 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: B 144 ASP cc_start: 0.8777 (t70) cc_final: 0.8509 (t70) REVERT: C 78 ILE cc_start: 0.4735 (OUTLIER) cc_final: 0.4311 (mt) REVERT: C 171 LYS cc_start: 0.7398 (tppt) cc_final: 0.7080 (tmtt) REVERT: C 177 MET cc_start: 0.6724 (mmt) cc_final: 0.6262 (tpt) REVERT: C 193 CYS cc_start: 0.7320 (t) cc_final: 0.6803 (m) REVERT: C 224 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.6855 (t80) REVERT: C 375 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5423 (mt) REVERT: D 97 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: D 136 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7868 (tp30) outliers start: 39 outliers final: 24 residues processed: 126 average time/residue: 0.1800 time to fit residues: 31.6485 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 224 TYR Chi-restraints excluded: chain A residue 241 GLN 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 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 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 224 TYR Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LEU 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 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 42 optimal weight: 0.0470 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7960 Z= 0.180 Angle : 0.557 6.378 10764 Z= 0.307 Chirality : 0.043 0.193 1140 Planarity : 0.005 0.051 1298 Dihedral : 8.857 56.920 1169 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.16 % Rotamer: Outliers : 4.07 % Allowed : 17.53 % Favored : 78.40 % 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: 0.61 (0.28), residues: 888 helix: 1.42 (0.21), residues: 556 sheet: 0.23 (0.64), residues: 58 loop : -1.71 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 371 HIS 0.008 0.001 HIS A 163 PHE 0.018 0.001 PHE A 135 TYR 0.028 0.001 TYR A 182 ARG 0.002 0.000 ARG C 112 ********************** 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 132 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.873 Fit side-chains REVERT: A 78 ILE cc_start: 0.4713 (OUTLIER) cc_final: 0.4283 (mt) REVERT: A 171 LYS cc_start: 0.7445 (tppt) cc_final: 0.7142 (tmtt) REVERT: A 177 MET cc_start: 0.6695 (mmt) cc_final: 0.6246 (tpt) REVERT: A 193 CYS cc_start: 0.7259 (t) cc_final: 0.6687 (m) REVERT: A 224 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.6794 (t80) REVERT: A 279 TYR cc_start: 0.7215 (m-10) cc_final: 0.6889 (m-10) REVERT: A 371 TRP cc_start: 0.5844 (OUTLIER) cc_final: 0.5204 (m-90) REVERT: A 375 ILE cc_start: 0.5768 (OUTLIER) cc_final: 0.5469 (mt) REVERT: B 19 LYS cc_start: 0.7434 (ptpp) cc_final: 0.7000 (ptpp) REVERT: B 97 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: C 78 ILE cc_start: 0.4721 (OUTLIER) cc_final: 0.4309 (mt) REVERT: C 171 LYS cc_start: 0.7350 (tppt) cc_final: 0.7044 (tmtt) REVERT: C 177 MET cc_start: 0.6701 (mmt) cc_final: 0.6251 (tpt) REVERT: C 193 CYS cc_start: 0.7282 (t) cc_final: 0.6736 (m) REVERT: C 224 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.6789 (t80) REVERT: C 279 TYR cc_start: 0.7167 (m-10) cc_final: 0.6769 (m-10) REVERT: C 371 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.5390 (m-90) REVERT: C 375 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5417 (mt) REVERT: D 97 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: D 136 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7845 (tp30) outliers start: 33 outliers final: 18 residues processed: 122 average time/residue: 0.1955 time to fit residues: 32.8289 Evaluate side-chains 127 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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 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 273 LYS 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 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 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.163264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135045 restraints weight = 9447.035| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.66 r_work: 0.3415 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7960 Z= 0.186 Angle : 0.560 6.433 10764 Z= 0.308 Chirality : 0.043 0.192 1140 Planarity : 0.005 0.051 1298 Dihedral : 8.608 56.769 1169 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.18 % Favored : 94.59 % Rotamer: Outliers : 3.70 % Allowed : 17.41 % 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: 0.71 (0.28), residues: 888 helix: 1.48 (0.21), residues: 558 sheet: 0.46 (0.65), residues: 58 loop : -1.69 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 371 HIS 0.008 0.001 HIS C 163 PHE 0.018 0.001 PHE A 135 TYR 0.050 0.002 TYR C 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: 2002.50 seconds wall clock time: 37 minutes 39.29 seconds (2259.29 seconds total)