Starting phenix.real_space_refine on Sun May 11 07:13:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2n_38858/05_2025/8y2n_38858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2n_38858/05_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_38858/05_2025/8y2n_38858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2n_38858/05_2025/8y2n_38858.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2n_38858/05_2025/8y2n_38858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2n_38858/05_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-5687/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: 5.83, per 1000 atoms: 0.76 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: 2.37 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: 0.59 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: 2.02 Time building geometry restraints manager: 2.66 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.700 Find NCS groups from input model: 0.130 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- 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 7964 Z= 0.558 Angle : 1.212 14.522 10772 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 Details of bonding type rmsd hydrogen bonds : bond 0.12579 ( 485) hydrogen bonds : angle 6.58689 ( 1431) SS BOND : bond 0.00604 ( 4) SS BOND : angle 0.27511 ( 8) covalent geometry : bond 0.01082 ( 7960) covalent geometry : angle 1.21273 (10764) *********************** 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 : 0.886 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: 0.2420 time to fit residues: 48.1683 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 : 0.842 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.165326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132234 restraints weight = 9494.650| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.21 r_work: 0.3401 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7964 Z= 0.180 Angle : 0.705 8.620 10772 Z= 0.387 Chirality : 0.048 0.256 1140 Planarity : 0.006 0.049 1298 Dihedral : 11.232 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 : 9.88 % 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: -0.26 (0.28), residues: 888 helix: 0.79 (0.22), residues: 560 sheet: -0.35 (0.66), residues: 58 loop : -2.14 (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 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 485) hydrogen bonds : angle 5.57347 ( 1431) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.31817 ( 8) covalent geometry : bond 0.00411 ( 7960) covalent geometry : angle 0.70536 (10764) *********************** 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 : 0.893 Fit side-chains REVERT: A 177 MET cc_start: 0.7324 (mmt) cc_final: 0.6687 (tpt) REVERT: A 193 CYS cc_start: 0.7553 (t) cc_final: 0.7070 (m) REVERT: A 205 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7500 (tptt) REVERT: A 371 TRP cc_start: 0.6016 (OUTLIER) cc_final: 0.5376 (m-90) REVERT: A 375 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.5905 (mt) REVERT: A 377 ARG cc_start: 0.6697 (ttp-170) cc_final: 0.5834 (tpt90) REVERT: B 134 ASP cc_start: 0.8586 (p0) cc_final: 0.8311 (p0) REVERT: C 89 MET cc_start: 0.7490 (mmt) cc_final: 0.7283 (mtt) REVERT: C 177 MET cc_start: 0.7312 (mmt) cc_final: 0.6650 (tpt) REVERT: C 193 CYS cc_start: 0.7511 (t) cc_final: 0.7000 (m) REVERT: C 205 LYS cc_start: 0.7724 (tmtt) cc_final: 0.7335 (tptt) REVERT: C 371 TRP cc_start: 0.6013 (OUTLIER) cc_final: 0.5348 (m-90) REVERT: C 375 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5943 (mt) REVERT: C 377 ARG cc_start: 0.6774 (ttp-170) cc_final: 0.5851 (tpt90) REVERT: D 134 ASP cc_start: 0.8608 (p0) cc_final: 0.8336 (p0) REVERT: D 136 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8009 (tp30) outliers start: 20 outliers final: 4 residues processed: 131 average time/residue: 0.2169 time to fit residues: 37.4703 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 : 0.858 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 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 = 0.3853 r_free = 0.3853 target = 0.161934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132432 restraints weight = 9553.353| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.75 r_work: 0.3420 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7964 Z= 0.160 Angle : 0.622 6.339 10772 Z= 0.342 Chirality : 0.045 0.230 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.910 59.848 1173 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.29 % Favored : 94.26 % Rotamer: Outliers : 3.70 % Allowed : 11.60 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.28), residues: 888 helix: 0.91 (0.21), residues: 568 sheet: -0.38 (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 0.006 0.001 HIS A 196 PHE 0.019 0.001 PHE A 135 TYR 0.029 0.002 TYR C 182 ARG 0.003 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 485) hydrogen bonds : angle 5.31438 ( 1431) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.31007 ( 8) covalent geometry : bond 0.00362 ( 7960) covalent geometry : angle 0.62235 (10764) *********************** 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 : 0.791 Fit side-chains REVERT: A 177 MET cc_start: 0.7489 (mmt) cc_final: 0.6777 (tpt) REVERT: A 193 CYS cc_start: 0.7672 (t) cc_final: 0.6946 (m) REVERT: A 205 LYS cc_start: 0.7884 (tmtt) cc_final: 0.7544 (tptt) REVERT: A 224 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7237 (t80) REVERT: A 371 TRP cc_start: 0.5819 (OUTLIER) cc_final: 0.5264 (m-90) REVERT: A 375 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5692 (mt) REVERT: A 377 ARG cc_start: 0.6775 (ttp80) cc_final: 0.5847 (tpt90) REVERT: B 134 ASP cc_start: 0.8519 (p0) cc_final: 0.8090 (p0) REVERT: C 89 MET cc_start: 0.7640 (mmt) cc_final: 0.7354 (mtt) REVERT: C 177 MET cc_start: 0.7424 (mmt) cc_final: 0.6715 (tpt) REVERT: C 193 CYS cc_start: 0.7679 (t) cc_final: 0.6959 (m) REVERT: C 205 LYS cc_start: 0.7799 (tmtt) cc_final: 0.6800 (mmtt) REVERT: C 224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 273 LYS cc_start: 0.8693 (mttm) cc_final: 0.8433 (mttt) REVERT: C 371 TRP cc_start: 0.5780 (OUTLIER) cc_final: 0.5235 (m-90) REVERT: C 375 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5711 (mt) REVERT: C 377 ARG cc_start: 0.6688 (ttp80) cc_final: 0.5778 (tpt90) REVERT: D 134 ASP cc_start: 0.8538 (p0) cc_final: 0.8119 (p0) outliers start: 30 outliers final: 12 residues processed: 143 average time/residue: 0.2109 time to fit residues: 40.2482 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 : 1.066 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.161469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131927 restraints weight = 9463.980| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.74 r_work: 0.3389 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7964 Z= 0.148 Angle : 0.588 6.336 10772 Z= 0.326 Chirality : 0.044 0.220 1140 Planarity : 0.005 0.051 1298 Dihedral : 10.523 59.877 1173 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.18 % Favored : 94.48 % Rotamer: Outliers : 4.44 % Allowed : 12.22 % 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: 0.20 (0.28), residues: 888 helix: 1.09 (0.21), residues: 568 sheet: -0.41 (0.62), residues: 58 loop : -1.86 (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 0.031 0.001 TYR C 182 ARG 0.002 0.000 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 485) hydrogen bonds : angle 5.21796 ( 1431) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.28975 ( 8) covalent geometry : bond 0.00334 ( 7960) covalent geometry : angle 0.58830 (10764) *********************** 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 151 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.021 Fit side-chains REVERT: A 78 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4459 (mt) REVERT: A 174 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5562 (ptm) REVERT: A 177 MET cc_start: 0.7376 (mmt) cc_final: 0.6719 (tpt) REVERT: A 193 CYS cc_start: 0.7644 (t) cc_final: 0.6891 (m) REVERT: A 224 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7193 (t80) REVERT: A 371 TRP cc_start: 0.5580 (OUTLIER) cc_final: 0.5160 (m-90) REVERT: A 375 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5632 (mt) REVERT: A 377 ARG cc_start: 0.6651 (ttp80) cc_final: 0.5642 (tpt90) REVERT: B 134 ASP cc_start: 0.8576 (p0) cc_final: 0.8146 (p0) REVERT: C 78 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4476 (mt) REVERT: C 89 MET cc_start: 0.7669 (mmt) cc_final: 0.7382 (mtt) REVERT: C 174 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5604 (ptm) REVERT: C 177 MET cc_start: 0.7368 (mmt) cc_final: 0.6715 (tpt) REVERT: C 193 CYS cc_start: 0.7642 (t) cc_final: 0.6914 (m) REVERT: C 224 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7277 (t80) REVERT: C 371 TRP cc_start: 0.5634 (OUTLIER) cc_final: 0.5147 (m-90) REVERT: C 375 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5615 (mt) REVERT: C 377 ARG cc_start: 0.6691 (ttp80) cc_final: 0.5694 (tpt90) REVERT: D 134 ASP cc_start: 0.8584 (p0) cc_final: 0.8162 (p0) outliers start: 36 outliers final: 12 residues processed: 135 average time/residue: 0.1910 time to fit residues: 35.5030 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.163578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134329 restraints weight = 9437.112| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.73 r_work: 0.3424 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7964 Z= 0.141 Angle : 0.566 6.252 10772 Z= 0.312 Chirality : 0.043 0.202 1140 Planarity : 0.005 0.052 1298 Dihedral : 10.088 59.745 1173 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 4.32 % Allowed : 13.70 % 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: 0.38 (0.28), residues: 888 helix: 1.30 (0.21), residues: 560 sheet: -0.37 (0.62), residues: 58 loop : -1.84 (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 A 196 PHE 0.019 0.001 PHE C 135 TYR 0.032 0.001 TYR A 182 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 485) hydrogen bonds : angle 5.11511 ( 1431) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.30735 ( 8) covalent geometry : bond 0.00313 ( 7960) covalent geometry : angle 0.56572 (10764) *********************** 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: 35 poor density : 120 time to evaluate : 0.783 Fit side-chains REVERT: A 78 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4501 (mt) REVERT: A 171 LYS cc_start: 0.7793 (tppt) cc_final: 0.7478 (tmtt) REVERT: A 174 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5546 (ptm) REVERT: A 177 MET cc_start: 0.7371 (mmt) cc_final: 0.6727 (tpt) REVERT: A 193 CYS cc_start: 0.7665 (t) cc_final: 0.6889 (m) REVERT: A 224 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7230 (t80) REVERT: A 371 TRP cc_start: 0.5400 (OUTLIER) cc_final: 0.5074 (m-90) REVERT: A 375 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5771 (mt) REVERT: A 377 ARG cc_start: 0.6583 (ttp80) cc_final: 0.5590 (tpt90) REVERT: B 97 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 108 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8459 (p0) REVERT: B 134 ASP cc_start: 0.8620 (p0) cc_final: 0.8135 (p0) REVERT: C 78 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4476 (mt) REVERT: C 89 MET cc_start: 0.7687 (mmt) cc_final: 0.7390 (mtt) REVERT: C 171 LYS cc_start: 0.7761 (tppt) cc_final: 0.7439 (tmtt) REVERT: C 174 MET cc_start: 0.5828 (OUTLIER) cc_final: 0.5543 (ptm) REVERT: C 177 MET cc_start: 0.7351 (mmt) cc_final: 0.6715 (tpt) REVERT: C 193 CYS cc_start: 0.7646 (t) cc_final: 0.6886 (m) REVERT: C 224 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7240 (t80) REVERT: C 371 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.5075 (m-90) REVERT: C 375 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5585 (mt) REVERT: C 377 ARG cc_start: 0.6550 (ttp80) cc_final: 0.5584 (tpt90) REVERT: D 97 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: D 108 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8481 (p0) REVERT: D 134 ASP cc_start: 0.8650 (p0) cc_final: 0.8177 (p0) outliers start: 35 outliers final: 15 residues processed: 138 average time/residue: 0.1824 time to fit residues: 34.8339 Evaluate side-chains 141 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 97 GLU 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: 0.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 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 = 0.3841 r_free = 0.3841 target = 0.161195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131910 restraints weight = 9516.900| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.72 r_work: 0.3392 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7964 Z= 0.145 Angle : 0.562 6.200 10772 Z= 0.310 Chirality : 0.043 0.209 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.819 59.530 1173 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 4.94 % Allowed : 14.57 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 888 helix: 1.33 (0.21), residues: 556 sheet: -0.15 (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 0.006 0.001 HIS A 163 PHE 0.018 0.001 PHE A 135 TYR 0.033 0.001 TYR C 182 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 485) hydrogen bonds : angle 5.08835 ( 1431) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.29717 ( 8) covalent geometry : bond 0.00328 ( 7960) covalent geometry : angle 0.56173 (10764) *********************** 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 154 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.791 Fit side-chains REVERT: A 78 ILE cc_start: 0.4974 (OUTLIER) cc_final: 0.4483 (mt) REVERT: A 123 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7518 (p) REVERT: A 171 LYS cc_start: 0.7645 (tppt) cc_final: 0.7363 (tmtt) REVERT: A 177 MET cc_start: 0.7477 (mmt) cc_final: 0.6824 (tpt) REVERT: A 193 CYS cc_start: 0.7729 (t) cc_final: 0.6993 (m) REVERT: A 224 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7284 (t80) REVERT: A 279 TYR cc_start: 0.7643 (m-10) cc_final: 0.7295 (m-10) REVERT: A 371 TRP cc_start: 0.5337 (OUTLIER) cc_final: 0.5031 (m-90) REVERT: A 375 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5723 (mt) REVERT: A 377 ARG cc_start: 0.6481 (ttp80) cc_final: 0.5525 (tpt90) REVERT: B 19 LYS cc_start: 0.7540 (ptpp) cc_final: 0.6687 (pttt) REVERT: B 97 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: B 108 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8479 (p0) REVERT: B 134 ASP cc_start: 0.8654 (p0) cc_final: 0.8159 (p0) REVERT: C 78 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.4468 (mt) REVERT: C 89 MET cc_start: 0.7633 (mmt) cc_final: 0.7390 (mtt) REVERT: C 123 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7522 (p) REVERT: C 171 LYS cc_start: 0.7648 (tppt) cc_final: 0.7365 (tmtt) REVERT: C 177 MET cc_start: 0.7437 (mmt) cc_final: 0.6799 (tpt) REVERT: C 193 CYS cc_start: 0.7630 (t) cc_final: 0.6911 (m) REVERT: C 224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 279 TYR cc_start: 0.7612 (m-10) cc_final: 0.7271 (m-10) REVERT: C 371 TRP cc_start: 0.5304 (OUTLIER) cc_final: 0.4981 (m-90) REVERT: C 375 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5699 (mt) REVERT: C 377 ARG cc_start: 0.6432 (ttp80) cc_final: 0.5484 (tpt90) REVERT: D 19 LYS cc_start: 0.7402 (ptpp) cc_final: 0.6679 (pttt) REVERT: D 97 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: D 108 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8451 (p0) outliers start: 40 outliers final: 18 residues processed: 138 average time/residue: 0.1916 time to fit residues: 36.1771 Evaluate side-chains 142 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 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: 9.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131443 restraints weight = 9433.682| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.70 r_work: 0.3369 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7964 Z= 0.166 Angle : 0.577 6.223 10772 Z= 0.318 Chirality : 0.044 0.224 1140 Planarity : 0.005 0.053 1298 Dihedral : 9.693 57.056 1173 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 5.31 % Allowed : 14.57 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 888 helix: 1.30 (0.21), residues: 556 sheet: -0.09 (0.62), residues: 58 loop : -1.99 (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 A 163 PHE 0.017 0.001 PHE C 135 TYR 0.036 0.002 TYR A 182 ARG 0.002 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 485) hydrogen bonds : angle 5.12686 ( 1431) SS BOND : bond 0.00293 ( 4) SS BOND : angle 0.31209 ( 8) covalent geometry : bond 0.00378 ( 7960) covalent geometry : angle 0.57727 (10764) *********************** 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: 43 poor density : 110 time to evaluate : 0.759 Fit side-chains REVERT: A 78 ILE cc_start: 0.5020 (OUTLIER) cc_final: 0.4513 (mt) REVERT: A 171 LYS cc_start: 0.7677 (tppt) cc_final: 0.7379 (tmtt) REVERT: A 177 MET cc_start: 0.7516 (mmt) cc_final: 0.6867 (tpt) REVERT: A 193 CYS cc_start: 0.7846 (t) cc_final: 0.7212 (m) REVERT: A 201 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 224 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7356 (t80) REVERT: A 371 TRP cc_start: 0.5322 (OUTLIER) cc_final: 0.5012 (m-90) REVERT: A 375 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5753 (mt) REVERT: A 377 ARG cc_start: 0.6548 (ttp80) cc_final: 0.5519 (tpt90) REVERT: B 97 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: B 108 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8556 (p0) REVERT: C 78 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4500 (mt) REVERT: C 89 MET cc_start: 0.7559 (mmt) cc_final: 0.7334 (mtt) REVERT: C 171 LYS cc_start: 0.7676 (tppt) cc_final: 0.7379 (tmtt) REVERT: C 177 MET cc_start: 0.7502 (mmt) cc_final: 0.6852 (tpt) REVERT: C 193 CYS cc_start: 0.7684 (t) cc_final: 0.7048 (m) REVERT: C 201 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: C 224 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7359 (t80) REVERT: C 371 TRP cc_start: 0.5297 (OUTLIER) cc_final: 0.4986 (m-90) REVERT: C 375 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5720 (mt) REVERT: C 377 ARG cc_start: 0.6543 (ttp80) cc_final: 0.5525 (tpt90) REVERT: D 19 LYS cc_start: 0.7467 (ptpp) cc_final: 0.6722 (pttt) REVERT: D 97 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: D 108 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8487 (p0) outliers start: 43 outliers final: 19 residues processed: 134 average time/residue: 0.1916 time to fit residues: 34.8744 Evaluate side-chains 144 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 97 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.161279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132342 restraints weight = 9581.075| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.71 r_work: 0.3423 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7964 Z= 0.137 Angle : 0.552 6.056 10772 Z= 0.305 Chirality : 0.043 0.201 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.386 56.816 1173 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.16 % Rotamer: Outliers : 4.69 % Allowed : 15.31 % Favored : 80.00 % 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: 1.39 (0.21), residues: 556 sheet: 0.04 (0.63), residues: 58 loop : -1.88 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 68 HIS 0.006 0.001 HIS C 163 PHE 0.018 0.001 PHE A 135 TYR 0.027 0.001 TYR C 182 ARG 0.002 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 485) hydrogen bonds : angle 5.06917 ( 1431) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.32608 ( 8) covalent geometry : bond 0.00296 ( 7960) covalent geometry : angle 0.55201 (10764) *********************** 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 146 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.782 Fit side-chains REVERT: A 78 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4478 (mt) REVERT: A 171 LYS cc_start: 0.7672 (tppt) cc_final: 0.7374 (tmtt) REVERT: A 177 MET cc_start: 0.7488 (mmt) cc_final: 0.6823 (tpt) REVERT: A 193 CYS cc_start: 0.7777 (t) cc_final: 0.7178 (m) REVERT: A 201 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 279 TYR cc_start: 0.7572 (m-10) cc_final: 0.7256 (m-10) REVERT: A 371 TRP cc_start: 0.5308 (OUTLIER) cc_final: 0.5029 (m-90) REVERT: A 375 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5776 (mt) REVERT: A 377 ARG cc_start: 0.6529 (ttp80) cc_final: 0.5500 (tpt90) REVERT: B 97 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: C 78 ILE cc_start: 0.4979 (OUTLIER) cc_final: 0.4515 (mt) REVERT: C 89 MET cc_start: 0.7536 (mmt) cc_final: 0.7322 (mtt) REVERT: C 171 LYS cc_start: 0.7666 (tppt) cc_final: 0.7369 (tmtt) REVERT: C 177 MET cc_start: 0.7472 (mmt) cc_final: 0.6815 (tpt) REVERT: C 193 CYS cc_start: 0.7647 (t) cc_final: 0.7049 (m) REVERT: C 201 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: C 224 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 279 TYR cc_start: 0.7557 (m-10) cc_final: 0.7239 (m-10) REVERT: C 371 TRP cc_start: 0.5278 (OUTLIER) cc_final: 0.4989 (m-90) REVERT: C 375 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5769 (mt) REVERT: C 377 ARG cc_start: 0.6529 (ttp80) cc_final: 0.5511 (tpt90) REVERT: D 97 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: D 136 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8028 (tp30) outliers start: 38 outliers final: 19 residues processed: 131 average time/residue: 0.1889 time to fit residues: 33.7868 Evaluate side-chains 138 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 174 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 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 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 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: 2.9990 chunk 80 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS C 241 GLN C 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134804 restraints weight = 9540.694| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.67 r_work: 0.3369 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7964 Z= 0.151 Angle : 0.562 6.180 10772 Z= 0.310 Chirality : 0.044 0.212 1140 Planarity : 0.005 0.052 1298 Dihedral : 9.277 56.688 1173 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.18 % Favored : 94.59 % Rotamer: Outliers : 3.95 % Allowed : 16.30 % 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: 0.60 (0.28), residues: 888 helix: 1.45 (0.21), residues: 556 sheet: 0.07 (0.63), residues: 58 loop : -1.77 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.008 0.001 HIS A 163 PHE 0.017 0.001 PHE C 135 TYR 0.029 0.001 TYR A 182 ARG 0.002 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 485) hydrogen bonds : angle 5.07448 ( 1431) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.29084 ( 8) covalent geometry : bond 0.00338 ( 7960) covalent geometry : angle 0.56256 (10764) *********************** 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 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.802 Fit side-chains REVERT: A 78 ILE cc_start: 0.4971 (OUTLIER) cc_final: 0.4487 (mt) REVERT: A 171 LYS cc_start: 0.7704 (tppt) cc_final: 0.7405 (tmtt) REVERT: A 177 MET cc_start: 0.7433 (mmt) cc_final: 0.6852 (tpt) REVERT: A 193 CYS cc_start: 0.7743 (t) cc_final: 0.7153 (m) REVERT: A 201 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: A 224 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7323 (t80) REVERT: A 279 TYR cc_start: 0.7641 (m-10) cc_final: 0.7285 (m-10) REVERT: A 371 TRP cc_start: 0.5254 (OUTLIER) cc_final: 0.4978 (m-90) REVERT: A 375 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5732 (mt) REVERT: A 377 ARG cc_start: 0.6407 (ttp80) cc_final: 0.5358 (tpt90) REVERT: B 97 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: C 78 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4511 (mt) REVERT: C 89 MET cc_start: 0.7454 (mmt) cc_final: 0.7249 (mtt) REVERT: C 171 LYS cc_start: 0.7655 (tppt) cc_final: 0.7351 (tmtt) REVERT: C 177 MET cc_start: 0.7415 (mmt) cc_final: 0.6843 (tpt) REVERT: C 193 CYS cc_start: 0.7710 (t) cc_final: 0.7135 (m) REVERT: C 201 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: C 224 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7317 (t80) REVERT: C 279 TYR cc_start: 0.7611 (m-10) cc_final: 0.7249 (m-10) REVERT: C 371 TRP cc_start: 0.5262 (OUTLIER) cc_final: 0.4989 (m-90) REVERT: C 375 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5756 (mt) REVERT: C 377 ARG cc_start: 0.6401 (ttp80) cc_final: 0.5366 (tpt90) REVERT: D 97 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7686 (tt0) outliers start: 32 outliers final: 19 residues processed: 123 average time/residue: 0.1992 time to fit residues: 33.3918 Evaluate side-chains 131 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 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 174 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 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 D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN C 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131906 restraints weight = 9579.017| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.66 r_work: 0.3352 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7964 Z= 0.202 Angle : 0.608 6.313 10772 Z= 0.334 Chirality : 0.046 0.247 1140 Planarity : 0.005 0.053 1298 Dihedral : 9.294 56.438 1170 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 4.20 % Allowed : 16.54 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 888 helix: 1.32 (0.21), residues: 556 sheet: 0.15 (0.63), residues: 58 loop : -1.75 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 371 HIS 0.008 0.002 HIS A 163 PHE 0.020 0.002 PHE A 333 TYR 0.037 0.002 TYR A 182 ARG 0.003 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 485) hydrogen bonds : angle 5.19053 ( 1431) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.46927 ( 8) covalent geometry : bond 0.00477 ( 7960) covalent geometry : angle 0.60825 (10764) ********************** 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 139 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.767 Fit side-chains REVERT: A 78 ILE cc_start: 0.4945 (OUTLIER) cc_final: 0.4454 (mt) REVERT: A 171 LYS cc_start: 0.7743 (tppt) cc_final: 0.7428 (tmtt) REVERT: A 177 MET cc_start: 0.7567 (mmt) cc_final: 0.6908 (tpt) REVERT: A 193 CYS cc_start: 0.7809 (t) cc_final: 0.7274 (m) REVERT: A 201 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: A 205 LYS cc_start: 0.7964 (tmtt) cc_final: 0.6793 (mmtt) REVERT: A 224 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7368 (t80) REVERT: A 279 TYR cc_start: 0.7687 (m-10) cc_final: 0.7337 (m-10) REVERT: A 371 TRP cc_start: 0.5369 (OUTLIER) cc_final: 0.5079 (m-90) REVERT: A 375 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5759 (mt) REVERT: B 97 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: C 78 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4479 (mt) REVERT: C 89 MET cc_start: 0.7591 (mmt) cc_final: 0.7320 (mtt) REVERT: C 171 LYS cc_start: 0.7727 (tppt) cc_final: 0.7417 (tmtt) REVERT: C 177 MET cc_start: 0.7546 (mmt) cc_final: 0.6889 (tpt) REVERT: C 193 CYS cc_start: 0.7780 (t) cc_final: 0.7266 (m) REVERT: C 201 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: C 205 LYS cc_start: 0.7905 (tmtt) cc_final: 0.6753 (mmtt) REVERT: C 224 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7383 (t80) REVERT: C 279 TYR cc_start: 0.7665 (m-10) cc_final: 0.7326 (m-10) REVERT: C 371 TRP cc_start: 0.5381 (OUTLIER) cc_final: 0.5086 (m-90) REVERT: C 375 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5741 (mt) REVERT: D 97 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7577 (tt0) outliers start: 34 outliers final: 16 residues processed: 130 average time/residue: 0.1931 time to fit residues: 34.1014 Evaluate side-chains 133 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 B residue 97 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 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 302 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 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 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 = 0.3877 r_free = 0.3877 target = 0.164006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135881 restraints weight = 9469.629| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.66 r_work: 0.3425 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7964 Z= 0.137 Angle : 0.559 5.952 10772 Z= 0.308 Chirality : 0.043 0.203 1140 Planarity : 0.005 0.052 1298 Dihedral : 8.980 57.337 1170 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 3.33 % Allowed : 17.16 % Favored : 79.51 % 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: 0.62 (0.28), residues: 888 helix: 1.45 (0.21), residues: 556 sheet: 0.37 (0.65), residues: 58 loop : -1.79 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 68 HIS 0.008 0.001 HIS A 163 PHE 0.019 0.001 PHE A 135 TYR 0.046 0.001 TYR C 182 ARG 0.003 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 485) hydrogen bonds : angle 5.09472 ( 1431) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.33496 ( 8) covalent geometry : bond 0.00295 ( 7960) covalent geometry : angle 0.55956 (10764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.05 seconds wall clock time: 76 minutes 4.83 seconds (4564.83 seconds total)