Starting phenix.real_space_refine on Fri Apr 5 20:27:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/04_2024/6zlv_11275.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 3380 2.51 5 N 944 2.21 5 O 1012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "B" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "C" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "D" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Time building chain proxies: 3.39, per 1000 atoms: 0.63 Number of scatterers: 5352 At special positions: 0 Unit cell: (75.978, 79.596, 121.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1012 8.00 N 944 7.00 C 3380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 14.3% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.586A pdb=" N GLU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'C' and resid 80 through 94 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 243 through 247 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 110 removed outlier: 4.218A pdb=" N GLY A 109 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 145 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 135 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.222A pdb=" N VAL A 236 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 239 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A 222 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER A 206 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.248A pdb=" N GLY B 109 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 145 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 135 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.209A pdb=" N VAL B 236 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 239 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 222 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER B 206 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.238A pdb=" N GLY C 109 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 145 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 135 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.241A pdb=" N VAL C 236 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 239 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 222 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 206 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 102 through 110 removed outlier: 4.209A pdb=" N GLY D 109 " --> pdb=" O MET D 120 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL D 145 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL D 135 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 164 through 169 removed outlier: 4.244A pdb=" N VAL D 236 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL D 239 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL D 222 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER D 206 " --> pdb=" O PRO D 218 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1121 1.33 - 1.45: 1188 1.45 - 1.57: 3088 1.57 - 1.70: 3 1.70 - 1.82: 32 Bond restraints: 5432 Sorted by residual: bond pdb=" C ILE B 108 " pdb=" N GLY B 109 " ideal model delta sigma weight residual 1.332 1.354 -0.022 6.60e-03 2.30e+04 1.16e+01 bond pdb=" C ILE C 108 " pdb=" N GLY C 109 " ideal model delta sigma weight residual 1.332 1.354 -0.022 6.60e-03 2.30e+04 1.08e+01 bond pdb=" C ILE D 108 " pdb=" N GLY D 109 " ideal model delta sigma weight residual 1.332 1.352 -0.020 6.60e-03 2.30e+04 9.55e+00 bond pdb=" C ILE A 108 " pdb=" N GLY A 109 " ideal model delta sigma weight residual 1.332 1.352 -0.020 6.60e-03 2.30e+04 9.09e+00 bond pdb=" C VAL A 236 " pdb=" O VAL A 236 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.09e-02 8.42e+03 8.70e+00 ... (remaining 5427 not shown) Histogram of bond angle deviations from ideal: 95.81 - 102.96: 52 102.96 - 110.11: 1199 110.11 - 117.26: 2913 117.26 - 124.41: 2944 124.41 - 131.55: 288 Bond angle restraints: 7396 Sorted by residual: angle pdb=" C THR A 82 " pdb=" N GLU A 83 " pdb=" CA GLU A 83 " ideal model delta sigma weight residual 120.54 128.15 -7.61 1.35e+00 5.49e-01 3.18e+01 angle pdb=" C THR C 82 " pdb=" N GLU C 83 " pdb=" CA GLU C 83 " ideal model delta sigma weight residual 120.54 128.11 -7.57 1.35e+00 5.49e-01 3.14e+01 angle pdb=" C THR D 82 " pdb=" N GLU D 83 " pdb=" CA GLU D 83 " ideal model delta sigma weight residual 120.54 128.06 -7.52 1.35e+00 5.49e-01 3.10e+01 angle pdb=" C THR B 82 " pdb=" N GLU B 83 " pdb=" CA GLU B 83 " ideal model delta sigma weight residual 120.54 127.97 -7.43 1.35e+00 5.49e-01 3.03e+01 angle pdb=" CB ARG D 175 " pdb=" CG ARG D 175 " pdb=" CD ARG D 175 " ideal model delta sigma weight residual 111.30 122.99 -11.69 2.30e+00 1.89e-01 2.58e+01 ... (remaining 7391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3103 15.79 - 31.57: 139 31.57 - 47.35: 60 47.35 - 63.14: 14 63.14 - 78.92: 4 Dihedral angle restraints: 3320 sinusoidal: 1308 harmonic: 2012 Sorted by residual: dihedral pdb=" C THR C 241 " pdb=" N THR C 241 " pdb=" CA THR C 241 " pdb=" CB THR C 241 " ideal model delta harmonic sigma weight residual -122.00 -132.49 10.49 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C THR A 241 " pdb=" N THR A 241 " pdb=" CA THR A 241 " pdb=" CB THR A 241 " ideal model delta harmonic sigma weight residual -122.00 -132.16 10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C THR B 241 " pdb=" N THR B 241 " pdb=" CA THR B 241 " pdb=" CB THR B 241 " ideal model delta harmonic sigma weight residual -122.00 -131.88 9.88 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 3317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 451 0.079 - 0.158: 276 0.158 - 0.237: 128 0.237 - 0.316: 27 0.316 - 0.395: 14 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA SER D 139 " pdb=" N SER D 139 " pdb=" C SER D 139 " pdb=" CB SER D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CG LEU B 204 " pdb=" CB LEU B 204 " pdb=" CD1 LEU B 204 " pdb=" CD2 LEU B 204 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA SER A 139 " pdb=" N SER A 139 " pdb=" C SER A 139 " pdb=" CB SER A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 893 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 108 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE D 108 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE D 108 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY D 109 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 108 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ILE B 108 " 0.072 2.00e-02 2.50e+03 pdb=" O ILE B 108 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY B 109 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 108 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ILE C 108 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE C 108 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY C 109 " -0.024 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 663 2.76 - 3.29: 5020 3.29 - 3.83: 8521 3.83 - 4.36: 10848 4.36 - 4.90: 18243 Nonbonded interactions: 43295 Sorted by model distance: nonbonded pdb=" OE1 GLU C 188 " pdb=" NH2 ARG D 190 " model vdw 2.221 2.520 nonbonded pdb=" NH2 ARG C 190 " pdb=" OE1 GLU D 188 " model vdw 2.230 2.520 nonbonded pdb=" OE1 GLN D 117 " pdb=" OG1 THR D 159 " model vdw 2.238 2.440 nonbonded pdb=" OE1 GLU A 188 " pdb=" NH2 ARG B 190 " model vdw 2.239 2.520 nonbonded pdb=" OE1 GLN B 117 " pdb=" OG1 THR B 159 " model vdw 2.240 2.440 ... (remaining 43290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 8.750 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 0.058 5432 Z= 0.689 Angle : 1.856 11.693 7396 Z= 1.212 Chirality : 0.120 0.395 896 Planarity : 0.010 0.049 972 Dihedral : 12.218 78.921 2024 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.74 % Favored : 95.69 % Rotamer: Outliers : 2.72 % Allowed : 4.25 % Favored : 93.03 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.30), residues: 696 helix: -3.69 (0.38), residues: 64 sheet: -0.88 (0.30), residues: 256 loop : -0.47 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS A 163 PHE 0.041 0.009 PHE A 115 TYR 0.054 0.013 TYR D 191 ARG 0.021 0.003 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6101 (tpt90) cc_final: 0.5707 (mmp-170) REVERT: A 97 LEU cc_start: 0.3451 (OUTLIER) cc_final: 0.1244 (tp) REVERT: A 125 GLU cc_start: 0.7596 (tp30) cc_final: 0.6680 (pt0) REVERT: A 133 GLN cc_start: 0.8409 (tt0) cc_final: 0.8189 (tt0) REVERT: A 147 GLU cc_start: 0.8762 (tt0) cc_final: 0.8471 (pt0) REVERT: A 152 THR cc_start: 0.8739 (p) cc_final: 0.8538 (t) REVERT: A 184 PRO cc_start: 0.9107 (Cg_exo) cc_final: 0.8879 (Cg_endo) REVERT: A 185 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7922 (tm-30) REVERT: B 83 GLU cc_start: 0.5305 (mm-30) cc_final: 0.4393 (pt0) REVERT: B 89 ARG cc_start: 0.6500 (tpt90) cc_final: 0.6070 (mmp-170) REVERT: B 97 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.1993 (tp) REVERT: B 125 GLU cc_start: 0.8238 (tp30) cc_final: 0.7563 (mt-10) REVERT: B 133 GLN cc_start: 0.8833 (tt0) cc_final: 0.8624 (tt0) REVERT: B 154 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8626 (ttm110) REVERT: C 89 ARG cc_start: 0.6160 (tpt90) cc_final: 0.5871 (mmp-170) REVERT: C 90 GLU cc_start: 0.7320 (tp30) cc_final: 0.7024 (tt0) REVERT: C 97 LEU cc_start: 0.3264 (OUTLIER) cc_final: 0.2134 (tp) REVERT: C 125 GLU cc_start: 0.7516 (tp30) cc_final: 0.6734 (pt0) REVERT: C 152 THR cc_start: 0.8683 (p) cc_final: 0.8443 (t) REVERT: C 154 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8401 (ttm-80) REVERT: D 89 ARG cc_start: 0.6474 (tpt90) cc_final: 0.5986 (mmp-170) REVERT: D 97 LEU cc_start: 0.3550 (OUTLIER) cc_final: 0.1669 (tp) REVERT: D 125 GLU cc_start: 0.8017 (tp30) cc_final: 0.7334 (pt0) REVERT: D 126 ASN cc_start: 0.7178 (m110) cc_final: 0.6535 (m110) REVERT: D 170 ASN cc_start: 0.6916 (t0) cc_final: 0.6026 (p0) REVERT: D 223 LYS cc_start: 0.9032 (tptt) cc_final: 0.8788 (tttm) outliers start: 16 outliers final: 0 residues processed: 174 average time/residue: 0.2321 time to fit residues: 49.1517 Evaluate side-chains 113 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 168 GLN B 144 GLN B 168 GLN C 113 ASN C 126 ASN C 144 GLN C 168 GLN D 144 GLN D 168 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5432 Z= 0.287 Angle : 0.706 5.328 7396 Z= 0.362 Chirality : 0.051 0.140 896 Planarity : 0.005 0.035 972 Dihedral : 5.618 36.423 772 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 7.99 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 696 helix: 0.74 (0.54), residues: 64 sheet: -0.43 (0.31), residues: 300 loop : 0.17 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 227 PHE 0.014 0.001 PHE A 115 TYR 0.011 0.002 TYR C 249 ARG 0.007 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.652 Fit side-chains REVERT: A 83 GLU cc_start: 0.4763 (mm-30) cc_final: 0.4052 (pt0) REVERT: A 89 ARG cc_start: 0.5839 (tpt90) cc_final: 0.5353 (mmp-170) REVERT: A 126 ASN cc_start: 0.7373 (m110) cc_final: 0.7009 (m110) REVERT: A 133 GLN cc_start: 0.8693 (tt0) cc_final: 0.8450 (tt0) REVERT: A 185 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7964 (tm-30) REVERT: B 83 GLU cc_start: 0.5188 (mm-30) cc_final: 0.4109 (pt0) REVERT: B 89 ARG cc_start: 0.5887 (tpt90) cc_final: 0.5309 (mpt180) REVERT: B 92 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4887 (mp) REVERT: B 97 LEU cc_start: 0.4063 (mp) cc_final: 0.3516 (mm) REVERT: B 125 GLU cc_start: 0.8476 (tp30) cc_final: 0.7996 (tm-30) REVERT: B 133 GLN cc_start: 0.9101 (tt0) cc_final: 0.8814 (tt0) REVERT: B 160 ASP cc_start: 0.7997 (t70) cc_final: 0.7744 (t70) REVERT: B 170 ASN cc_start: 0.7555 (t0) cc_final: 0.7211 (p0) REVERT: C 89 ARG cc_start: 0.5683 (tpt90) cc_final: 0.5350 (mpt180) REVERT: C 90 GLU cc_start: 0.7718 (tp30) cc_final: 0.7338 (tt0) REVERT: C 125 GLU cc_start: 0.8104 (tp30) cc_final: 0.7807 (tm-30) REVERT: C 149 MET cc_start: 0.7464 (mpp) cc_final: 0.6808 (mpp) REVERT: C 154 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8139 (ttm-80) REVERT: D 83 GLU cc_start: 0.4984 (mm-30) cc_final: 0.4354 (pt0) REVERT: D 89 ARG cc_start: 0.6459 (tpt90) cc_final: 0.5918 (mmp-170) REVERT: D 125 GLU cc_start: 0.8566 (tp30) cc_final: 0.8172 (tm-30) REVERT: D 170 ASN cc_start: 0.7159 (t0) cc_final: 0.6411 (p0) REVERT: D 195 THR cc_start: 0.8794 (p) cc_final: 0.8487 (t) outliers start: 16 outliers final: 5 residues processed: 122 average time/residue: 0.2296 time to fit residues: 34.2925 Evaluate side-chains 94 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5432 Z= 0.256 Angle : 0.682 6.859 7396 Z= 0.336 Chirality : 0.049 0.135 896 Planarity : 0.005 0.033 972 Dihedral : 4.548 15.037 764 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 10.20 % Favored : 87.07 % 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 (0.32), residues: 696 helix: 2.77 (0.62), residues: 64 sheet: -0.41 (0.31), residues: 288 loop : 0.57 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 163 PHE 0.007 0.001 PHE A 254 TYR 0.010 0.002 TYR A 249 ARG 0.004 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.4699 (mm-30) cc_final: 0.3756 (pt0) REVERT: A 89 ARG cc_start: 0.5874 (tpt90) cc_final: 0.5230 (mmp-170) REVERT: A 185 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8045 (tm-30) REVERT: B 83 GLU cc_start: 0.5394 (mm-30) cc_final: 0.4266 (pt0) REVERT: B 89 ARG cc_start: 0.6063 (tpt90) cc_final: 0.5325 (mmp-170) REVERT: B 92 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4958 (mp) REVERT: B 125 GLU cc_start: 0.8574 (tp30) cc_final: 0.8205 (tm-30) REVERT: C 83 GLU cc_start: 0.5706 (mm-30) cc_final: 0.4478 (pt0) REVERT: C 89 ARG cc_start: 0.5508 (tpt90) cc_final: 0.4971 (mmp-170) REVERT: C 125 GLU cc_start: 0.8404 (tp30) cc_final: 0.8165 (tm-30) REVERT: C 149 MET cc_start: 0.7147 (mpp) cc_final: 0.6410 (mpp) REVERT: D 83 GLU cc_start: 0.5134 (mm-30) cc_final: 0.4452 (pt0) REVERT: D 89 ARG cc_start: 0.6383 (tpt90) cc_final: 0.5686 (mmp-170) REVERT: D 125 GLU cc_start: 0.8646 (tp30) cc_final: 0.8214 (tm-30) REVERT: D 170 ASN cc_start: 0.7247 (t0) cc_final: 0.6577 (p0) REVERT: D 195 THR cc_start: 0.8778 (p) cc_final: 0.8492 (t) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.2400 time to fit residues: 31.1709 Evaluate side-chains 93 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 37 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5432 Z= 0.244 Angle : 0.660 6.946 7396 Z= 0.323 Chirality : 0.049 0.135 896 Planarity : 0.005 0.031 972 Dihedral : 4.469 15.543 764 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.57 % Allowed : 11.22 % Favored : 85.20 % 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: 0.30 (0.33), residues: 696 helix: 3.32 (0.62), residues: 64 sheet: -0.75 (0.30), residues: 284 loop : 0.65 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 163 PHE 0.005 0.001 PHE D 115 TYR 0.007 0.001 TYR A 249 ARG 0.005 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.4898 (mm-30) cc_final: 0.3828 (pt0) REVERT: A 89 ARG cc_start: 0.5488 (tpt90) cc_final: 0.4907 (mmp-170) REVERT: A 126 ASN cc_start: 0.8101 (m110) cc_final: 0.7703 (m-40) REVERT: B 83 GLU cc_start: 0.5369 (mm-30) cc_final: 0.4159 (pt0) REVERT: B 89 ARG cc_start: 0.6200 (tpt90) cc_final: 0.5390 (mmp-170) REVERT: B 92 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.5041 (mp) REVERT: B 125 GLU cc_start: 0.8823 (tp30) cc_final: 0.8438 (tm-30) REVERT: C 83 GLU cc_start: 0.5787 (mm-30) cc_final: 0.4468 (pt0) REVERT: C 89 ARG cc_start: 0.5388 (tpt90) cc_final: 0.4710 (mmp-170) REVERT: C 149 MET cc_start: 0.6839 (mpp) cc_final: 0.6368 (mpp) REVERT: D 83 GLU cc_start: 0.5406 (mm-30) cc_final: 0.4506 (pt0) REVERT: D 89 ARG cc_start: 0.6043 (tpt90) cc_final: 0.5390 (mmp-170) REVERT: D 103 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7043 (tt) REVERT: D 125 GLU cc_start: 0.8817 (tp30) cc_final: 0.8498 (tm-30) REVERT: D 170 ASN cc_start: 0.7451 (t0) cc_final: 0.6919 (p0) outliers start: 21 outliers final: 11 residues processed: 108 average time/residue: 0.2125 time to fit residues: 28.3907 Evaluate side-chains 93 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5432 Z= 0.183 Angle : 0.607 7.396 7396 Z= 0.300 Chirality : 0.047 0.130 896 Planarity : 0.004 0.029 972 Dihedral : 4.238 14.412 764 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.55 % Allowed : 11.90 % Favored : 85.54 % 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: 0.30 (0.32), residues: 696 helix: 3.47 (0.59), residues: 64 sheet: -0.86 (0.30), residues: 284 loop : 0.73 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 227 PHE 0.008 0.001 PHE A 115 TYR 0.011 0.001 TYR B 249 ARG 0.006 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.4882 (mm-30) cc_final: 0.3852 (pt0) REVERT: A 89 ARG cc_start: 0.5273 (tpt90) cc_final: 0.4630 (mmp-170) REVERT: A 125 GLU cc_start: 0.8099 (tp30) cc_final: 0.7864 (mm-30) REVERT: A 126 ASN cc_start: 0.8247 (m110) cc_final: 0.7745 (m-40) REVERT: B 83 GLU cc_start: 0.5443 (mm-30) cc_final: 0.4285 (pt0) REVERT: B 89 ARG cc_start: 0.6207 (tpt90) cc_final: 0.5413 (mmp-170) REVERT: B 92 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.5011 (mp) REVERT: B 125 GLU cc_start: 0.8805 (tp30) cc_final: 0.8490 (tm-30) REVERT: C 83 GLU cc_start: 0.5803 (mm-30) cc_final: 0.4480 (pt0) REVERT: C 89 ARG cc_start: 0.5398 (tpt90) cc_final: 0.4696 (mmp-170) REVERT: D 83 GLU cc_start: 0.5580 (mm-30) cc_final: 0.4675 (pt0) REVERT: D 89 ARG cc_start: 0.6054 (tpt90) cc_final: 0.5373 (mmp-170) REVERT: D 103 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6971 (tt) REVERT: D 125 GLU cc_start: 0.8827 (tp30) cc_final: 0.8474 (tm-30) REVERT: D 170 ASN cc_start: 0.7556 (t0) cc_final: 0.7071 (p0) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.2263 time to fit residues: 28.4596 Evaluate side-chains 92 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN D 117 GLN D 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5432 Z= 0.241 Angle : 0.650 7.387 7396 Z= 0.317 Chirality : 0.048 0.138 896 Planarity : 0.004 0.029 972 Dihedral : 4.431 15.910 764 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.57 % Allowed : 12.41 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.33), residues: 696 helix: 3.53 (0.59), residues: 64 sheet: -0.99 (0.29), residues: 284 loop : 0.69 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 163 PHE 0.006 0.001 PHE A 115 TYR 0.008 0.001 TYR C 249 ARG 0.006 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.4981 (mm-30) cc_final: 0.3919 (pt0) REVERT: A 89 ARG cc_start: 0.5419 (tpt90) cc_final: 0.4734 (mmp-170) REVERT: A 126 ASN cc_start: 0.8320 (m110) cc_final: 0.7885 (m-40) REVERT: A 223 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8453 (ttpt) REVERT: B 83 GLU cc_start: 0.5544 (mm-30) cc_final: 0.4369 (pt0) REVERT: B 89 ARG cc_start: 0.6257 (tpt90) cc_final: 0.5457 (mmp-170) REVERT: B 92 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.5051 (mp) REVERT: B 125 GLU cc_start: 0.8811 (tp30) cc_final: 0.8454 (tm-30) REVERT: C 83 GLU cc_start: 0.6078 (mm-30) cc_final: 0.4726 (pt0) REVERT: C 89 ARG cc_start: 0.5477 (tpt90) cc_final: 0.4704 (mmp-170) REVERT: C 125 GLU cc_start: 0.8596 (tt0) cc_final: 0.8306 (tm-30) REVERT: D 83 GLU cc_start: 0.5630 (mm-30) cc_final: 0.4645 (pt0) REVERT: D 89 ARG cc_start: 0.6167 (tpt90) cc_final: 0.5404 (mmp-170) REVERT: D 113 ASN cc_start: 0.8748 (t0) cc_final: 0.8536 (t0) REVERT: D 125 GLU cc_start: 0.8795 (tp30) cc_final: 0.8344 (mt-10) REVERT: D 170 ASN cc_start: 0.7377 (t0) cc_final: 0.6883 (p0) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.2229 time to fit residues: 28.2209 Evaluate side-chains 95 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 0.0370 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.7266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5432 Z= 0.179 Angle : 0.618 6.864 7396 Z= 0.302 Chirality : 0.047 0.142 896 Planarity : 0.004 0.026 972 Dihedral : 4.323 16.292 764 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.72 % Allowed : 14.12 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.33), residues: 696 helix: 3.62 (0.58), residues: 64 sheet: -0.99 (0.29), residues: 284 loop : 0.76 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 227 PHE 0.006 0.000 PHE A 115 TYR 0.009 0.001 TYR D 151 ARG 0.006 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.5093 (mm-30) cc_final: 0.4063 (pt0) REVERT: A 89 ARG cc_start: 0.5446 (tpt90) cc_final: 0.4748 (mmp-170) REVERT: A 126 ASN cc_start: 0.8344 (m110) cc_final: 0.7814 (m-40) REVERT: B 83 GLU cc_start: 0.5591 (mm-30) cc_final: 0.4369 (pt0) REVERT: B 89 ARG cc_start: 0.6186 (tpt90) cc_final: 0.5422 (mmp-170) REVERT: B 92 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.5098 (mp) REVERT: B 125 GLU cc_start: 0.8774 (tp30) cc_final: 0.8458 (tm-30) REVERT: C 83 GLU cc_start: 0.6149 (mm-30) cc_final: 0.4826 (pt0) REVERT: C 89 ARG cc_start: 0.5384 (tpt90) cc_final: 0.4608 (mmp-170) REVERT: C 125 GLU cc_start: 0.8611 (tt0) cc_final: 0.8310 (tm-30) REVERT: D 83 GLU cc_start: 0.5423 (mm-30) cc_final: 0.4502 (pt0) REVERT: D 89 ARG cc_start: 0.5931 (tpt90) cc_final: 0.5227 (mmp-170) REVERT: D 113 ASN cc_start: 0.8719 (t0) cc_final: 0.8483 (t0) REVERT: D 125 GLU cc_start: 0.8767 (tp30) cc_final: 0.8370 (mt-10) REVERT: D 149 MET cc_start: 0.6845 (mtm) cc_final: 0.6556 (mpp) REVERT: D 170 ASN cc_start: 0.7540 (t0) cc_final: 0.7074 (p0) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.2396 time to fit residues: 30.1232 Evaluate side-chains 93 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 6 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5432 Z= 0.184 Angle : 0.632 7.001 7396 Z= 0.307 Chirality : 0.047 0.141 896 Planarity : 0.004 0.026 972 Dihedral : 4.322 18.579 764 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.89 % Allowed : 14.97 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.33), residues: 696 helix: 3.69 (0.58), residues: 64 sheet: -1.02 (0.29), residues: 284 loop : 0.90 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 227 PHE 0.006 0.001 PHE A 115 TYR 0.011 0.001 TYR D 249 ARG 0.005 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.5088 (mm-30) cc_final: 0.4056 (pt0) REVERT: A 89 ARG cc_start: 0.5372 (tpt90) cc_final: 0.4693 (mmp-170) REVERT: A 126 ASN cc_start: 0.8366 (m110) cc_final: 0.7850 (m-40) REVERT: B 83 GLU cc_start: 0.5571 (mm-30) cc_final: 0.4345 (pt0) REVERT: B 89 ARG cc_start: 0.6159 (tpt90) cc_final: 0.5469 (mmp-170) REVERT: B 92 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5109 (mp) REVERT: B 125 GLU cc_start: 0.8734 (tp30) cc_final: 0.8425 (tm-30) REVERT: C 83 GLU cc_start: 0.6158 (mm-30) cc_final: 0.4836 (pt0) REVERT: C 89 ARG cc_start: 0.5386 (tpt90) cc_final: 0.4621 (mmp-170) REVERT: C 125 GLU cc_start: 0.8644 (tt0) cc_final: 0.8347 (tm-30) REVERT: D 83 GLU cc_start: 0.5448 (mm-30) cc_final: 0.4560 (pt0) REVERT: D 89 ARG cc_start: 0.5863 (tpt90) cc_final: 0.5102 (mmp-170) REVERT: D 125 GLU cc_start: 0.8768 (tp30) cc_final: 0.8416 (mt-10) REVERT: D 126 ASN cc_start: 0.8247 (m110) cc_final: 0.7995 (m-40) REVERT: D 149 MET cc_start: 0.6730 (mtm) cc_final: 0.6423 (mpp) REVERT: D 170 ASN cc_start: 0.7529 (t0) cc_final: 0.7080 (p0) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.2261 time to fit residues: 26.0045 Evaluate side-chains 91 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5432 Z= 0.232 Angle : 0.665 7.117 7396 Z= 0.322 Chirality : 0.048 0.142 896 Planarity : 0.004 0.028 972 Dihedral : 4.438 16.371 764 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.72 % Allowed : 14.63 % Favored : 82.65 % 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: 0.29 (0.33), residues: 696 helix: 3.58 (0.59), residues: 64 sheet: -1.06 (0.29), residues: 284 loop : 0.91 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 163 PHE 0.006 0.001 PHE A 115 TYR 0.010 0.001 TYR D 249 ARG 0.007 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.5046 (mm-30) cc_final: 0.3935 (pt0) REVERT: A 89 ARG cc_start: 0.5349 (tpt90) cc_final: 0.4681 (mmp-170) REVERT: A 126 ASN cc_start: 0.8473 (m110) cc_final: 0.7960 (m-40) REVERT: B 83 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4291 (pt0) REVERT: B 89 ARG cc_start: 0.6148 (tpt90) cc_final: 0.5517 (mmp-170) REVERT: B 92 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5137 (mp) REVERT: B 125 GLU cc_start: 0.8772 (tp30) cc_final: 0.8494 (tm-30) REVERT: C 83 GLU cc_start: 0.6099 (mm-30) cc_final: 0.4835 (pt0) REVERT: C 89 ARG cc_start: 0.5460 (tpt90) cc_final: 0.4736 (mmp-170) REVERT: C 125 GLU cc_start: 0.8703 (tt0) cc_final: 0.8411 (tm-30) REVERT: D 83 GLU cc_start: 0.5535 (mm-30) cc_final: 0.4634 (pt0) REVERT: D 89 ARG cc_start: 0.5713 (tpt90) cc_final: 0.4947 (mmp-170) REVERT: D 125 GLU cc_start: 0.8754 (tp30) cc_final: 0.8396 (mt-10) REVERT: D 126 ASN cc_start: 0.8258 (m110) cc_final: 0.7753 (m-40) REVERT: D 149 MET cc_start: 0.6874 (mtm) cc_final: 0.6549 (mpp) REVERT: D 170 ASN cc_start: 0.7427 (t0) cc_final: 0.6935 (p0) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.2190 time to fit residues: 24.8438 Evaluate side-chains 91 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5432 Z= 0.224 Angle : 0.662 7.314 7396 Z= 0.321 Chirality : 0.048 0.137 896 Planarity : 0.004 0.028 972 Dihedral : 4.440 17.543 764 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.55 % Allowed : 14.80 % Favored : 82.65 % 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: 0.29 (0.33), residues: 696 helix: 3.45 (0.58), residues: 64 sheet: -1.09 (0.29), residues: 284 loop : 0.96 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 227 PHE 0.007 0.001 PHE A 115 TYR 0.007 0.001 TYR C 249 ARG 0.005 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.5344 (tpt90) cc_final: 0.4683 (mmp-170) REVERT: A 125 GLU cc_start: 0.8341 (tp30) cc_final: 0.8106 (mm-30) REVERT: A 126 ASN cc_start: 0.8503 (m110) cc_final: 0.7935 (m-40) REVERT: B 89 ARG cc_start: 0.6140 (tpt90) cc_final: 0.5529 (mmp-170) REVERT: B 92 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5100 (mp) REVERT: B 125 GLU cc_start: 0.8739 (tp30) cc_final: 0.8500 (tm-30) REVERT: C 83 GLU cc_start: 0.6112 (mm-30) cc_final: 0.4829 (pt0) REVERT: C 89 ARG cc_start: 0.5438 (tpt90) cc_final: 0.4734 (mmp-170) REVERT: C 125 GLU cc_start: 0.8705 (tt0) cc_final: 0.8400 (tm-30) REVERT: D 83 GLU cc_start: 0.5597 (mm-30) cc_final: 0.4697 (pt0) REVERT: D 89 ARG cc_start: 0.5754 (tpt90) cc_final: 0.4992 (mmp-170) REVERT: D 125 GLU cc_start: 0.8735 (tp30) cc_final: 0.8473 (mt-10) REVERT: D 126 ASN cc_start: 0.8261 (m110) cc_final: 0.7776 (m-40) REVERT: D 149 MET cc_start: 0.6888 (mtm) cc_final: 0.6493 (mpp) REVERT: D 170 ASN cc_start: 0.7303 (t0) cc_final: 0.6801 (p0) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.2232 time to fit residues: 25.6414 Evaluate side-chains 92 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 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 = 0.3452 r_free = 0.3452 target = 0.076856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062313 restraints weight = 11370.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064535 restraints weight = 6802.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066048 restraints weight = 4813.108| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5432 Z= 0.231 Angle : 0.679 9.515 7396 Z= 0.330 Chirality : 0.048 0.148 896 Planarity : 0.004 0.028 972 Dihedral : 4.478 19.058 764 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 15.31 % Favored : 82.31 % 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 (0.33), residues: 696 helix: 3.28 (0.58), residues: 64 sheet: -1.13 (0.29), residues: 284 loop : 0.96 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 163 PHE 0.007 0.001 PHE A 115 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG D 186 =============================================================================== Job complete usr+sys time: 1458.19 seconds wall clock time: 26 minutes 55.58 seconds (1615.58 seconds total)