Starting phenix.real_space_refine on Tue Feb 13 12:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/02_2024/8gyx_34379_updated.pdb" } resolution = 3.7 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= 0.004 sd= 0.108 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 4050 2.51 5 N 978 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 313": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6118 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.84, per 1000 atoms: 0.63 Number of scatterers: 6118 At special positions: 0 Unit cell: (108.07, 90.95, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 4 11.99 O 1036 8.00 N 978 7.00 C 4050 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 78 removed outlier: 3.966A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 Processing helix chain 'B' and resid 116 through 142 removed outlier: 3.600A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.595A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 179 through 203 Processing helix chain 'B' and resid 213 through 236 removed outlier: 3.540A pdb=" N LEU B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 246 through 271 Proline residue: B 250 - end of helix removed outlier: 3.702A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 306 removed outlier: 4.200A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 339 Processing helix chain 'B' and resid 349 through 362 removed outlier: 4.007A pdb=" N GLY B 353 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 354 - end of helix removed outlier: 3.601A pdb=" N LEU B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 361 " --> pdb=" O PHE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 399 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.967A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 Processing helix chain 'A' and resid 116 through 142 removed outlier: 3.600A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.596A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 203 Processing helix chain 'A' and resid 213 through 236 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 246 through 271 Proline residue: A 250 - end of helix removed outlier: 3.703A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.200A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 362 removed outlier: 4.006A pdb=" N GLY A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.600A pdb=" N LEU A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 361 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 376 hydrogen bonds defined for protein. 1104 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: 1.45 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 898 1.32 - 1.44: 1812 1.44 - 1.57: 3498 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6286 Sorted by residual: bond pdb=" O12 POV A 501 " pdb=" P POV A 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O12 POV B 501 " pdb=" P POV B 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.80e+00 bond pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.77e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.529 1.567 -0.038 1.62e-02 3.81e+03 5.49e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 172 105.83 - 112.90: 3084 112.90 - 119.97: 2448 119.97 - 127.04: 2740 127.04 - 134.11: 100 Bond angle restraints: 8544 Sorted by residual: angle pdb=" CB MET A 339 " pdb=" CG MET A 339 " pdb=" SD MET A 339 " ideal model delta sigma weight residual 112.70 130.88 -18.18 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CB MET B 339 " pdb=" CG MET B 339 " pdb=" SD MET B 339 " ideal model delta sigma weight residual 112.70 130.87 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 104.61 7.39 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" CD PRO A 148 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.76e+01 angle pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 8539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 3233 18.09 - 36.17: 305 36.17 - 54.26: 90 54.26 - 72.34: 20 72.34 - 90.43: 6 Dihedral angle restraints: 3654 sinusoidal: 1446 harmonic: 2208 Sorted by residual: dihedral pdb=" C ASN B 144 " pdb=" N ASN B 144 " pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" C ASN A 144 " pdb=" N ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " pdb=" OD1 ASP B 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.29 59.29 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 796 0.082 - 0.164: 142 0.164 - 0.245: 34 0.245 - 0.327: 2 0.327 - 0.409: 4 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB ILE B 222 " pdb=" CA ILE B 222 " pdb=" CG1 ILE B 222 " pdb=" CG2 ILE B 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" C PRO A 148 " pdb=" CB PRO A 148 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 975 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 501 " -0.096 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C29 POV B 501 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV B 501 " -0.325 2.00e-02 2.50e+03 pdb="C211 POV B 501 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 501 " 0.096 2.00e-02 2.50e+03 2.38e-01 5.66e+02 pdb=" C29 POV A 501 " -0.317 2.00e-02 2.50e+03 pdb="C210 POV A 501 " 0.325 2.00e-02 2.50e+03 pdb="C211 POV A 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 147 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 148 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " -0.057 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 322 2.75 - 3.28: 6541 3.28 - 3.82: 10137 3.82 - 4.36: 11820 4.36 - 4.90: 20133 Nonbonded interactions: 48953 Sorted by model distance: nonbonded pdb=" OD1 ASP A 133 " pdb="MG MG A 502 " model vdw 2.208 2.170 nonbonded pdb=" OD1 ASP B 133 " pdb="MG MG B 502 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP B 158 " pdb="MG MG B 503 " model vdw 2.234 2.170 nonbonded pdb=" OD2 ASP A 158 " pdb="MG MG A 503 " model vdw 2.235 2.170 nonbonded pdb=" OG1 THR A 143 " pdb=" OG SER A 145 " model vdw 2.261 2.440 ... (remaining 48948 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' } 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: 0.460 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.990 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.780 Find NCS groups from input model: 0.300 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.007 0.060 6286 Z= 0.439 Angle : 1.358 18.179 8544 Z= 0.780 Chirality : 0.072 0.409 978 Planarity : 0.014 0.238 1040 Dihedral : 16.071 90.426 2230 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.64 % Favored : 80.06 % 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: 1.06 (0.28), residues: 756 helix: 0.85 (0.20), residues: 548 sheet: None (None), residues: 0 loop : 0.67 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 74 HIS 0.031 0.004 HIS A 46 PHE 0.056 0.003 PHE B 260 TYR 0.046 0.005 TYR B 387 ARG 0.014 0.003 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.803 Fit side-chains REVERT: B 131 SER cc_start: 0.8853 (m) cc_final: 0.8614 (m) REVERT: B 267 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7433 (ptm160) REVERT: A 131 SER cc_start: 0.8866 (m) cc_final: 0.8658 (m) outliers start: 2 outliers final: 2 residues processed: 164 average time/residue: 0.2055 time to fit residues: 42.8641 Evaluate side-chains 160 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain A residue 149 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 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 130 GLN B 197 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 57 GLN A 130 GLN A 197 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6286 Z= 0.183 Angle : 0.588 9.888 8544 Z= 0.302 Chirality : 0.042 0.154 978 Planarity : 0.005 0.057 1040 Dihedral : 10.861 88.184 898 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.72 % Allowed : 19.34 % Favored : 77.95 % 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: 2.78 (0.29), residues: 756 helix: 2.11 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 1.22 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 117 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.001 PHE B 187 TYR 0.013 0.001 TYR B 319 ARG 0.004 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 267 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7626 (ptm160) REVERT: B 339 MET cc_start: 0.8804 (mmm) cc_final: 0.8584 (mmm) REVERT: B 347 HIS cc_start: 0.8144 (p90) cc_final: 0.7578 (p90) REVERT: B 360 ASP cc_start: 0.9079 (t70) cc_final: 0.8782 (t0) REVERT: A 347 HIS cc_start: 0.8172 (p90) cc_final: 0.7393 (p-80) REVERT: A 360 ASP cc_start: 0.9085 (t70) cc_final: 0.8789 (t0) outliers start: 18 outliers final: 12 residues processed: 196 average time/residue: 0.1994 time to fit residues: 49.5411 Evaluate side-chains 185 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 224 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 224 HIS ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.006 0.039 6286 Z= 0.371 Angle : 0.660 7.586 8544 Z= 0.347 Chirality : 0.047 0.156 978 Planarity : 0.005 0.045 1040 Dihedral : 10.870 85.150 898 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 6.80 % Allowed : 18.73 % Favored : 74.47 % 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: 2.54 (0.29), residues: 756 helix: 1.94 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 1.14 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 181 HIS 0.005 0.001 HIS B 338 PHE 0.027 0.002 PHE A 234 TYR 0.019 0.002 TYR A 201 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 0.636 Fit side-chains REVERT: B 98 CYS cc_start: 0.8640 (m) cc_final: 0.8047 (m) REVERT: B 119 TYR cc_start: 0.8855 (m-10) cc_final: 0.8580 (m-10) REVERT: B 195 CYS cc_start: 0.8819 (t) cc_final: 0.8569 (t) REVERT: B 199 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 252 LEU cc_start: 0.9001 (mt) cc_final: 0.8785 (mt) REVERT: B 381 PHE cc_start: 0.8512 (t80) cc_final: 0.7889 (t80) REVERT: A 98 CYS cc_start: 0.8645 (m) cc_final: 0.8032 (m) REVERT: A 138 LYS cc_start: 0.8848 (mttp) cc_final: 0.8545 (mttm) REVERT: A 195 CYS cc_start: 0.8820 (t) cc_final: 0.8582 (t) REVERT: A 199 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8448 (tm-30) REVERT: A 252 LEU cc_start: 0.8991 (mt) cc_final: 0.8750 (mt) REVERT: A 305 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8684 (mmmt) REVERT: A 381 PHE cc_start: 0.8485 (t80) cc_final: 0.7897 (t80) outliers start: 45 outliers final: 32 residues processed: 243 average time/residue: 0.1603 time to fit residues: 51.9667 Evaluate side-chains 234 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6286 Z= 0.193 Angle : 0.566 6.129 8544 Z= 0.292 Chirality : 0.041 0.156 978 Planarity : 0.004 0.035 1040 Dihedral : 10.302 80.483 894 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.63 % Allowed : 26.28 % Favored : 70.09 % 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: 2.74 (0.30), residues: 756 helix: 2.12 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 1.07 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 117 HIS 0.003 0.001 HIS B 46 PHE 0.016 0.001 PHE A 187 TYR 0.014 0.001 TYR A 201 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 0.642 Fit side-chains REVERT: B 212 ASP cc_start: 0.8288 (t0) cc_final: 0.8052 (m-30) REVERT: B 219 PHE cc_start: 0.7413 (t80) cc_final: 0.7062 (m-10) REVERT: B 252 LEU cc_start: 0.9009 (mt) cc_final: 0.8748 (mt) REVERT: B 381 PHE cc_start: 0.8439 (t80) cc_final: 0.7798 (t80) REVERT: A 138 LYS cc_start: 0.8691 (mttp) cc_final: 0.8434 (mttp) REVERT: A 212 ASP cc_start: 0.8283 (t0) cc_final: 0.8045 (m-30) REVERT: A 219 PHE cc_start: 0.7467 (t80) cc_final: 0.7204 (t80) REVERT: A 252 LEU cc_start: 0.9000 (mt) cc_final: 0.8731 (mt) REVERT: A 305 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8670 (mmmt) REVERT: A 339 MET cc_start: 0.8937 (mmm) cc_final: 0.8700 (mmm) REVERT: A 381 PHE cc_start: 0.8352 (t80) cc_final: 0.7724 (t80) outliers start: 24 outliers final: 13 residues processed: 206 average time/residue: 0.1393 time to fit residues: 39.6975 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6286 Z= 0.230 Angle : 0.554 5.656 8544 Z= 0.292 Chirality : 0.042 0.184 978 Planarity : 0.004 0.034 1040 Dihedral : 9.952 81.416 894 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.29 % Allowed : 26.74 % Favored : 67.98 % 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: 2.75 (0.30), residues: 756 helix: 2.12 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.14 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 117 HIS 0.003 0.001 HIS B 46 PHE 0.026 0.002 PHE B 234 TYR 0.021 0.002 TYR B 387 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.702 Fit side-chains REVERT: B 199 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 212 ASP cc_start: 0.8328 (t0) cc_final: 0.8066 (m-30) REVERT: B 219 PHE cc_start: 0.7427 (t80) cc_final: 0.7050 (m-10) REVERT: B 252 LEU cc_start: 0.9033 (mt) cc_final: 0.8749 (mt) REVERT: B 381 PHE cc_start: 0.8467 (t80) cc_final: 0.7830 (t80) REVERT: A 50 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7605 (ttt180) REVERT: A 95 ILE cc_start: 0.8631 (tp) cc_final: 0.8400 (mt) REVERT: A 199 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 212 ASP cc_start: 0.8327 (t0) cc_final: 0.8082 (m-30) REVERT: A 219 PHE cc_start: 0.7501 (t80) cc_final: 0.7260 (t80) REVERT: A 252 LEU cc_start: 0.9040 (mt) cc_final: 0.8767 (mt) REVERT: A 305 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8714 (mmmt) REVERT: A 381 PHE cc_start: 0.8411 (t80) cc_final: 0.7760 (t80) REVERT: A 387 TYR cc_start: 0.8256 (t80) cc_final: 0.8053 (t80) outliers start: 35 outliers final: 35 residues processed: 216 average time/residue: 0.1734 time to fit residues: 49.5535 Evaluate side-chains 220 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6286 Z= 0.174 Angle : 0.562 9.058 8544 Z= 0.289 Chirality : 0.041 0.189 978 Planarity : 0.004 0.033 1040 Dihedral : 9.715 79.858 894 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.68 % Allowed : 27.64 % Favored : 67.67 % 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: 2.81 (0.30), residues: 756 helix: 2.15 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 1.18 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 117 HIS 0.002 0.001 HIS B 197 PHE 0.017 0.001 PHE A 187 TYR 0.021 0.001 TYR B 387 ARG 0.007 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7616 (ttt180) REVERT: B 78 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8042 (mmm160) REVERT: B 95 ILE cc_start: 0.8641 (tp) cc_final: 0.8402 (mt) REVERT: B 199 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 219 PHE cc_start: 0.7405 (t80) cc_final: 0.7093 (m-10) REVERT: B 252 LEU cc_start: 0.9056 (mt) cc_final: 0.8769 (mt) REVERT: B 339 MET cc_start: 0.8873 (mmm) cc_final: 0.8597 (mmm) REVERT: B 345 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7164 (m170) REVERT: B 381 PHE cc_start: 0.8406 (t80) cc_final: 0.7746 (t80) REVERT: A 139 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8879 (tm-30) REVERT: A 219 PHE cc_start: 0.7410 (t80) cc_final: 0.6986 (m-10) REVERT: A 252 LEU cc_start: 0.9040 (mt) cc_final: 0.8758 (mt) REVERT: A 305 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8774 (mmmt) REVERT: A 381 PHE cc_start: 0.8339 (t80) cc_final: 0.7689 (t80) outliers start: 31 outliers final: 27 residues processed: 218 average time/residue: 0.1955 time to fit residues: 54.4303 Evaluate side-chains 221 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6286 Z= 0.196 Angle : 0.598 11.417 8544 Z= 0.298 Chirality : 0.042 0.199 978 Planarity : 0.004 0.034 1040 Dihedral : 9.517 80.632 894 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.98 % Allowed : 28.40 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.30), residues: 756 helix: 2.14 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.03 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.002 0.001 HIS B 197 PHE 0.017 0.001 PHE A 187 TYR 0.021 0.001 TYR B 387 ARG 0.008 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8050 (mmm160) REVERT: B 219 PHE cc_start: 0.7420 (t80) cc_final: 0.7084 (m-10) REVERT: B 244 ILE cc_start: 0.8183 (tp) cc_final: 0.7782 (mm) REVERT: B 252 LEU cc_start: 0.9082 (mt) cc_final: 0.8803 (mt) REVERT: B 281 ILE cc_start: 0.8350 (tt) cc_final: 0.8002 (tp) REVERT: B 345 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7063 (m170) REVERT: B 381 PHE cc_start: 0.8422 (t80) cc_final: 0.7764 (t80) REVERT: A 50 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7638 (ttt180) REVERT: A 139 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8874 (tm-30) REVERT: A 199 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 219 PHE cc_start: 0.7538 (t80) cc_final: 0.7136 (m-10) REVERT: A 252 LEU cc_start: 0.9024 (mt) cc_final: 0.8726 (mt) REVERT: A 281 ILE cc_start: 0.8325 (tt) cc_final: 0.7948 (tp) REVERT: A 345 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6773 (m170) REVERT: A 381 PHE cc_start: 0.8357 (t80) cc_final: 0.7708 (t80) outliers start: 33 outliers final: 31 residues processed: 216 average time/residue: 0.1943 time to fit residues: 53.4154 Evaluate side-chains 216 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6286 Z= 0.245 Angle : 0.633 12.416 8544 Z= 0.314 Chirality : 0.043 0.199 978 Planarity : 0.005 0.033 1040 Dihedral : 9.433 83.131 894 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 7.10 % Allowed : 26.28 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.30), residues: 756 helix: 2.11 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 1.06 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 235 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.001 PHE B 187 TYR 0.020 0.002 TYR B 387 ARG 0.008 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LYS cc_start: 0.8677 (tttt) cc_final: 0.8098 (ttmt) REVERT: B 50 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7660 (ttt180) REVERT: B 199 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 246 MET cc_start: 0.7021 (ttp) cc_final: 0.6735 (tmm) REVERT: B 252 LEU cc_start: 0.9109 (mt) cc_final: 0.8825 (mt) REVERT: B 281 ILE cc_start: 0.8429 (tt) cc_final: 0.8068 (tp) REVERT: B 345 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7196 (m170) REVERT: B 381 PHE cc_start: 0.8464 (t80) cc_final: 0.8081 (t80) REVERT: A 50 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7645 (ttt180) REVERT: A 199 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 252 LEU cc_start: 0.9073 (mt) cc_final: 0.8770 (mt) REVERT: A 281 ILE cc_start: 0.8435 (tt) cc_final: 0.8070 (tp) REVERT: A 345 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7148 (m170) REVERT: A 381 PHE cc_start: 0.8380 (t80) cc_final: 0.7722 (t80) outliers start: 47 outliers final: 41 residues processed: 212 average time/residue: 0.1754 time to fit residues: 48.4511 Evaluate side-chains 232 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6286 Z= 0.168 Angle : 0.612 10.752 8544 Z= 0.299 Chirality : 0.041 0.195 978 Planarity : 0.004 0.033 1040 Dihedral : 9.330 81.140 894 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.44 % Allowed : 27.64 % Favored : 66.92 % 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: 2.94 (0.30), residues: 756 helix: 2.23 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.31 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 117 HIS 0.002 0.001 HIS B 197 PHE 0.017 0.001 PHE A 187 TYR 0.018 0.001 TYR B 387 ARG 0.008 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7756 (ttt180) REVERT: B 78 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8100 (mmm160) REVERT: B 199 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 252 LEU cc_start: 0.9030 (mt) cc_final: 0.8707 (mt) REVERT: B 281 ILE cc_start: 0.8216 (tt) cc_final: 0.7936 (tp) REVERT: B 339 MET cc_start: 0.8375 (mmm) cc_final: 0.8110 (mmm) REVERT: B 345 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7354 (m170) REVERT: B 381 PHE cc_start: 0.8363 (t80) cc_final: 0.7733 (t80) REVERT: A 50 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7667 (ttt180) REVERT: A 199 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 244 ILE cc_start: 0.8011 (tp) cc_final: 0.7665 (mm) REVERT: A 252 LEU cc_start: 0.9014 (mt) cc_final: 0.8690 (mt) REVERT: A 281 ILE cc_start: 0.8239 (tt) cc_final: 0.7949 (tp) REVERT: A 345 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7211 (m170) REVERT: A 381 PHE cc_start: 0.8304 (t80) cc_final: 0.7659 (t80) outliers start: 36 outliers final: 32 residues processed: 212 average time/residue: 0.1901 time to fit residues: 51.6346 Evaluate side-chains 221 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6286 Z= 0.188 Angle : 0.622 10.614 8544 Z= 0.306 Chirality : 0.041 0.205 978 Planarity : 0.005 0.038 1040 Dihedral : 9.288 81.442 894 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.14 % Allowed : 29.15 % Favored : 65.71 % 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: 2.86 (0.30), residues: 756 helix: 2.21 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 1.12 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 117 HIS 0.002 0.001 HIS B 197 PHE 0.016 0.001 PHE A 187 TYR 0.019 0.001 TYR B 387 ARG 0.009 0.001 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7741 (ttt180) REVERT: B 78 ARG cc_start: 0.8339 (mmm160) cc_final: 0.8112 (mmm160) REVERT: B 199 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 244 ILE cc_start: 0.8053 (tp) cc_final: 0.7651 (mm) REVERT: B 252 LEU cc_start: 0.9053 (mt) cc_final: 0.8726 (mt) REVERT: B 281 ILE cc_start: 0.8201 (tt) cc_final: 0.7917 (tp) REVERT: B 339 MET cc_start: 0.8357 (mmm) cc_final: 0.8091 (mmm) REVERT: B 345 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7281 (m170) REVERT: B 381 PHE cc_start: 0.8396 (t80) cc_final: 0.7747 (t80) REVERT: A 50 ARG cc_start: 0.8294 (ttm110) cc_final: 0.7776 (ttt180) REVERT: A 244 ILE cc_start: 0.8108 (tp) cc_final: 0.7704 (mm) REVERT: A 245 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6281 (tp-100) REVERT: A 252 LEU cc_start: 0.9025 (mt) cc_final: 0.8700 (mt) REVERT: A 281 ILE cc_start: 0.8246 (tt) cc_final: 0.7973 (tp) REVERT: A 345 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7331 (m170) REVERT: A 381 PHE cc_start: 0.8322 (t80) cc_final: 0.7695 (t80) outliers start: 34 outliers final: 31 residues processed: 209 average time/residue: 0.2106 time to fit residues: 56.7260 Evaluate side-chains 221 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 245 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118874 restraints weight = 7756.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124209 restraints weight = 4075.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127681 restraints weight = 2770.253| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6286 Z= 0.278 Angle : 0.653 10.239 8544 Z= 0.327 Chirality : 0.043 0.184 978 Planarity : 0.005 0.037 1040 Dihedral : 9.295 84.239 894 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.44 % Allowed : 28.85 % Favored : 65.71 % 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: 2.76 (0.30), residues: 756 helix: 2.12 (0.20), residues: 566 sheet: None (None), residues: 0 loop : 1.15 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS B 46 PHE 0.028 0.002 PHE A 105 TYR 0.018 0.002 TYR B 387 ARG 0.009 0.001 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.10 seconds wall clock time: 29 minutes 48.01 seconds (1788.01 seconds total)