Starting phenix.real_space_refine on Sat May 10 01:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua3_42049/05_2025/8ua3_42049.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 24 5.16 5 C 2835 2.51 5 N 746 2.21 5 O 845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4450 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2517 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain breaks: 1 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Time building chain proxies: 4.38, per 1000 atoms: 0.98 Number of scatterers: 4450 At special positions: 0 Unit cell: (80.64, 95.76, 80.64, 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 24 16.00 O 845 8.00 N 746 7.00 C 2835 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 593.8 milliseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 8 sheets defined 31.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.898A pdb=" N GLU C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.593A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.829A pdb=" N GLN C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.603A pdb=" N LEU C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.521A pdb=" N PHE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.622A pdb=" N VAL D 20 " --> pdb=" O HIS D 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.610A pdb=" N ALA D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 removed outlier: 3.600A pdb=" N PHE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.574A pdb=" N GLU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 Processing helix chain 'E' and resid 51 through 56 removed outlier: 4.218A pdb=" N SER E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.719A pdb=" N VAL E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.541A pdb=" N ILE E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.693A pdb=" N TYR C 104 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 148 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 106 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 145 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 261 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY C 147 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 257 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 168 removed outlier: 5.977A pdb=" N GLY C 321 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N PHE C 357 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET C 323 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY C 359 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 325 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.768A pdb=" N GLY C 274 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY C 224 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.780A pdb=" N VAL C 219 " --> pdb=" O PHE C 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 362 through 363 removed outlier: 3.667A pdb=" N GLU C 362 " --> pdb=" O HIS C 388 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS C 388 " --> pdb=" O GLU C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AA7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.702A pdb=" N VAL D 36 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 37 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU D 75 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE D 39 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 40 135 hydrogen bonds defined for protein. 366 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: 1.02 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 761 1.29 - 1.42: 1138 1.42 - 1.55: 2599 1.55 - 1.68: 4 1.68 - 1.81: 31 Bond restraints: 4533 Sorted by residual: bond pdb=" CG PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 1.503 1.157 0.346 3.40e-02 8.65e+02 1.04e+02 bond pdb=" N PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" CB PRO D 86 " pdb=" CG PRO D 86 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.82e+00 bond pdb=" N PRO D 86 " pdb=" CA PRO D 86 " ideal model delta sigma weight residual 1.472 1.438 0.034 1.34e-02 5.57e+03 6.31e+00 bond pdb=" CA ARG E 28 " pdb=" C ARG E 28 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.30e-02 5.92e+03 3.72e+00 ... (remaining 4528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 6088 3.59 - 7.18: 38 7.18 - 10.77: 2 10.77 - 14.36: 1 14.36 - 17.96: 2 Bond angle restraints: 6131 Sorted by residual: angle pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 112.00 94.95 17.05 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO D 86 " pdb=" CD PRO D 86 " pdb=" CG PRO D 86 " ideal model delta sigma weight residual 103.20 85.24 17.96 1.50e+00 4.44e-01 1.43e+02 angle pdb=" CA PRO D 86 " pdb=" CB PRO D 86 " pdb=" CG PRO D 86 " ideal model delta sigma weight residual 104.50 92.33 12.17 1.90e+00 2.77e-01 4.10e+01 angle pdb=" N TYR D 58 " pdb=" CA TYR D 58 " pdb=" C TYR D 58 " ideal model delta sigma weight residual 114.04 107.44 6.60 1.24e+00 6.50e-01 2.83e+01 angle pdb=" N PRO D 86 " pdb=" CA PRO D 86 " pdb=" CB PRO D 86 " ideal model delta sigma weight residual 103.26 97.72 5.54 1.14e+00 7.69e-01 2.36e+01 ... (remaining 6126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 2230 16.74 - 33.49: 361 33.49 - 50.23: 89 50.23 - 66.97: 23 66.97 - 83.71: 7 Dihedral angle restraints: 2710 sinusoidal: 1064 harmonic: 1646 Sorted by residual: dihedral pdb=" CA VAL C 381 " pdb=" C VAL C 381 " pdb=" N LYS C 382 " pdb=" CA LYS C 382 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLU D 41 " pdb=" C GLU D 41 " pdb=" N GLY D 42 " pdb=" CA GLY D 42 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG C 203 " pdb=" C ARG C 203 " pdb=" N HIS C 204 " pdb=" CA HIS C 204 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 2707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 400 0.031 - 0.062: 189 0.062 - 0.092: 70 0.092 - 0.123: 34 0.123 - 0.154: 15 Chirality restraints: 708 Sorted by residual: chirality pdb=" CB ILE E 118 " pdb=" CA ILE E 118 " pdb=" CG1 ILE E 118 " pdb=" CG2 ILE E 118 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CG LEU E 33 " pdb=" CB LEU E 33 " pdb=" CD1 LEU E 33 " pdb=" CD2 LEU E 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA LEU C 201 " pdb=" N LEU C 201 " pdb=" C LEU C 201 " pdb=" CB LEU C 201 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 705 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 85 " -0.112 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO D 86 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 75 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO D 76 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 76 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 76 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 90 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.29e+00 pdb=" CD GLU C 90 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU C 90 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 90 " -0.011 2.00e-02 2.50e+03 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 207 2.71 - 3.26: 4460 3.26 - 3.81: 6817 3.81 - 4.35: 8407 4.35 - 4.90: 13987 Nonbonded interactions: 33878 Sorted by model distance: nonbonded pdb=" OD1 ASP C 107 " pdb=" N SER C 108 " model vdw 2.166 3.120 nonbonded pdb=" OG SER C 263 " pdb=" OD1 ASN C 266 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP C 298 " pdb=" OG1 THR C 301 " model vdw 2.211 3.040 nonbonded pdb=" O VAL C 240 " pdb=" OG SER C 244 " model vdw 2.211 3.040 nonbonded pdb=" NH2 ARG C 346 " pdb=" O PRO C 350 " model vdw 2.214 3.120 ... (remaining 33873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 7 through 127) selection = chain 'E' } 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: 7.260 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 0.346 4533 Z= 0.254 Angle : 0.923 17.956 6131 Z= 0.577 Chirality : 0.047 0.154 708 Planarity : 0.007 0.152 793 Dihedral : 18.048 83.712 1642 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.65 % Favored : 91.81 % Rotamer: Outliers : 0.60 % Allowed : 30.52 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.35), residues: 562 helix: -1.21 (0.40), residues: 172 sheet: -0.08 (0.55), residues: 106 loop : -2.29 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 68 HIS 0.004 0.001 HIS E 16 PHE 0.026 0.002 PHE C 373 TYR 0.026 0.001 TYR C 334 ARG 0.015 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.27900 ( 135) hydrogen bonds : angle 10.13075 ( 366) covalent geometry : bond 0.00672 ( 4533) covalent geometry : angle 0.92299 ( 6131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.500 Fit side-chains REVERT: C 94 ASN cc_start: 0.4771 (OUTLIER) cc_final: 0.4458 (m-40) REVERT: C 247 ASN cc_start: 0.7839 (p0) cc_final: 0.7585 (p0) REVERT: D 14 SER cc_start: 0.8678 (p) cc_final: 0.8356 (t) REVERT: E 77 GLU cc_start: 0.7206 (pm20) cc_final: 0.6786 (pm20) REVERT: E 104 ASP cc_start: 0.8158 (t0) cc_final: 0.7706 (t0) outliers start: 3 outliers final: 1 residues processed: 117 average time/residue: 0.1570 time to fit residues: 23.3664 Evaluate side-chains 80 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 94 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159946 restraints weight = 5492.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161373 restraints weight = 4248.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163925 restraints weight = 3528.658| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4533 Z= 0.160 Angle : 0.686 10.082 6131 Z= 0.367 Chirality : 0.049 0.151 708 Planarity : 0.005 0.065 793 Dihedral : 5.924 46.652 603 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.19 % Favored : 91.46 % Rotamer: Outliers : 4.02 % Allowed : 29.12 % Favored : 66.87 % 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: -2.22 (0.35), residues: 562 helix: -1.12 (0.39), residues: 185 sheet: 0.27 (0.54), residues: 109 loop : -2.54 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 68 HIS 0.006 0.001 HIS C 398 PHE 0.012 0.002 PHE D 112 TYR 0.009 0.001 TYR E 11 ARG 0.007 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 135) hydrogen bonds : angle 6.95850 ( 366) covalent geometry : bond 0.00363 ( 4533) covalent geometry : angle 0.68613 ( 6131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: C 129 MET cc_start: 0.6468 (mpp) cc_final: 0.5428 (ttm) REVERT: C 347 LYS cc_start: 0.7360 (tptm) cc_final: 0.6822 (tttp) REVERT: E 44 ARG cc_start: 0.8272 (mtp85) cc_final: 0.8047 (mtp85) outliers start: 20 outliers final: 12 residues processed: 102 average time/residue: 0.1456 time to fit residues: 19.2800 Evaluate side-chains 88 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.171067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138530 restraints weight = 5387.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138409 restraints weight = 5442.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141578 restraints weight = 5056.097| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4533 Z= 0.152 Angle : 0.658 9.973 6131 Z= 0.347 Chirality : 0.048 0.144 708 Planarity : 0.004 0.038 793 Dihedral : 5.360 23.608 600 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.19 % Favored : 91.46 % Rotamer: Outliers : 4.42 % Allowed : 29.72 % Favored : 65.86 % 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: -2.04 (0.35), residues: 562 helix: -0.82 (0.39), residues: 182 sheet: 0.05 (0.54), residues: 115 loop : -2.43 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 68 HIS 0.005 0.001 HIS C 398 PHE 0.016 0.001 PHE E 112 TYR 0.009 0.001 TYR E 11 ARG 0.007 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 135) hydrogen bonds : angle 6.26735 ( 366) covalent geometry : bond 0.00357 ( 4533) covalent geometry : angle 0.65810 ( 6131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: C 94 ASN cc_start: 0.5110 (OUTLIER) cc_final: 0.4901 (m-40) REVERT: C 129 MET cc_start: 0.6146 (mpp) cc_final: 0.5249 (ttm) REVERT: C 347 LYS cc_start: 0.7235 (tptm) cc_final: 0.6966 (tttp) REVERT: E 44 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7894 (mtp85) outliers start: 22 outliers final: 14 residues processed: 96 average time/residue: 0.1593 time to fit residues: 19.6764 Evaluate side-chains 90 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 51 optimal weight: 0.0570 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** 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 = 0.3984 r_free = 0.3984 target = 0.174214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139479 restraints weight = 5320.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139764 restraints weight = 4912.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142450 restraints weight = 4674.469| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4533 Z= 0.117 Angle : 0.622 12.316 6131 Z= 0.322 Chirality : 0.046 0.144 708 Planarity : 0.003 0.034 793 Dihedral : 5.168 24.150 600 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 4.42 % Allowed : 29.92 % Favored : 65.66 % 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: -1.83 (0.36), residues: 562 helix: -0.58 (0.41), residues: 178 sheet: 0.06 (0.53), residues: 115 loop : -2.27 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 68 HIS 0.004 0.001 HIS C 398 PHE 0.010 0.001 PHE D 112 TYR 0.007 0.001 TYR C 104 ARG 0.008 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 135) hydrogen bonds : angle 5.91976 ( 366) covalent geometry : bond 0.00270 ( 4533) covalent geometry : angle 0.62217 ( 6131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.509 Fit side-chains REVERT: C 129 MET cc_start: 0.6105 (mpp) cc_final: 0.5309 (ttm) REVERT: E 44 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7928 (mtp85) outliers start: 22 outliers final: 18 residues processed: 101 average time/residue: 0.1502 time to fit residues: 19.7210 Evaluate side-chains 96 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN C 163 ASN C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153290 restraints weight = 5611.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153634 restraints weight = 4228.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157276 restraints weight = 3776.095| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4533 Z= 0.175 Angle : 0.673 11.959 6131 Z= 0.349 Chirality : 0.048 0.162 708 Planarity : 0.004 0.039 793 Dihedral : 5.358 22.914 600 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 5.82 % Allowed : 30.32 % Favored : 63.86 % 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: -1.90 (0.35), residues: 562 helix: -0.75 (0.40), residues: 183 sheet: 0.23 (0.54), residues: 110 loop : -2.31 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 68 HIS 0.005 0.001 HIS C 398 PHE 0.022 0.002 PHE D 9 TYR 0.011 0.002 TYR E 11 ARG 0.010 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 135) hydrogen bonds : angle 6.01768 ( 366) covalent geometry : bond 0.00411 ( 4533) covalent geometry : angle 0.67269 ( 6131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.479 Fit side-chains REVERT: C 226 ASN cc_start: 0.7982 (m-40) cc_final: 0.6934 (t0) REVERT: C 394 MET cc_start: 0.8346 (mmm) cc_final: 0.7683 (mmm) REVERT: D 7 SER cc_start: 0.7117 (OUTLIER) cc_final: 0.6549 (p) REVERT: E 44 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8088 (mtp85) REVERT: E 62 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8260 (mmt90) outliers start: 29 outliers final: 21 residues processed: 101 average time/residue: 0.1707 time to fit residues: 21.6067 Evaluate side-chains 99 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 0.2980 chunk 34 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154239 restraints weight = 5499.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157510 restraints weight = 4345.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158470 restraints weight = 3279.021| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4533 Z= 0.132 Angle : 0.667 13.782 6131 Z= 0.338 Chirality : 0.047 0.147 708 Planarity : 0.004 0.047 793 Dihedral : 5.244 24.179 600 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.65 % Favored : 92.17 % Rotamer: Outliers : 5.62 % Allowed : 31.12 % Favored : 63.25 % 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: -1.88 (0.35), residues: 562 helix: -0.65 (0.40), residues: 182 sheet: 0.14 (0.53), residues: 112 loop : -2.35 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 68 HIS 0.004 0.001 HIS C 388 PHE 0.022 0.001 PHE D 9 TYR 0.021 0.002 TYR C 225 ARG 0.010 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 135) hydrogen bonds : angle 5.92322 ( 366) covalent geometry : bond 0.00311 ( 4533) covalent geometry : angle 0.66676 ( 6131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.482 Fit side-chains REVERT: C 226 ASN cc_start: 0.7978 (m-40) cc_final: 0.6962 (t0) REVERT: C 394 MET cc_start: 0.8381 (mmm) cc_final: 0.7774 (mmm) REVERT: D 7 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6665 (p) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.1610 time to fit residues: 21.1036 Evaluate side-chains 101 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 123 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.191360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153610 restraints weight = 5563.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156652 restraints weight = 4537.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157635 restraints weight = 3422.200| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4533 Z= 0.177 Angle : 0.713 13.634 6131 Z= 0.363 Chirality : 0.048 0.162 708 Planarity : 0.004 0.051 793 Dihedral : 5.302 23.355 600 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.07 % Favored : 90.75 % Rotamer: Outliers : 5.82 % Allowed : 30.52 % Favored : 63.65 % 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: -1.92 (0.35), residues: 562 helix: -0.60 (0.39), residues: 182 sheet: -0.01 (0.53), residues: 112 loop : -2.36 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 68 HIS 0.005 0.001 HIS C 398 PHE 0.018 0.002 PHE D 9 TYR 0.020 0.002 TYR C 225 ARG 0.012 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 135) hydrogen bonds : angle 5.92465 ( 366) covalent geometry : bond 0.00422 ( 4533) covalent geometry : angle 0.71311 ( 6131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.515 Fit side-chains REVERT: C 226 ASN cc_start: 0.7984 (m-40) cc_final: 0.7041 (t0) REVERT: C 249 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 375 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 105 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7593 (mm-30) outliers start: 29 outliers final: 23 residues processed: 105 average time/residue: 0.1717 time to fit residues: 22.7026 Evaluate side-chains 106 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 123 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154567 restraints weight = 5512.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157632 restraints weight = 4683.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159082 restraints weight = 3351.599| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4533 Z= 0.133 Angle : 0.686 13.242 6131 Z= 0.347 Chirality : 0.047 0.170 708 Planarity : 0.004 0.054 793 Dihedral : 5.178 23.528 600 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.01 % Favored : 91.81 % Rotamer: Outliers : 5.42 % Allowed : 31.53 % Favored : 63.05 % 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: -1.78 (0.35), residues: 562 helix: -0.39 (0.40), residues: 181 sheet: 0.20 (0.53), residues: 110 loop : -2.39 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 68 HIS 0.004 0.001 HIS C 398 PHE 0.019 0.001 PHE D 9 TYR 0.022 0.002 TYR C 225 ARG 0.012 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 135) hydrogen bonds : angle 5.86482 ( 366) covalent geometry : bond 0.00312 ( 4533) covalent geometry : angle 0.68586 ( 6131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.497 Fit side-chains REVERT: C 226 ASN cc_start: 0.8028 (m-40) cc_final: 0.7086 (t0) REVERT: C 375 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8102 (tt) REVERT: C 394 MET cc_start: 0.8124 (mmm) cc_final: 0.7796 (mtp) REVERT: D 7 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.6897 (p) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.1629 time to fit residues: 21.9240 Evaluate side-chains 104 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155228 restraints weight = 5523.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158236 restraints weight = 4604.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159292 restraints weight = 3416.940| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4533 Z= 0.145 Angle : 0.697 13.025 6131 Z= 0.353 Chirality : 0.048 0.184 708 Planarity : 0.004 0.049 793 Dihedral : 5.130 23.371 600 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Rotamer: Outliers : 5.22 % Allowed : 31.33 % Favored : 63.45 % 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: -1.69 (0.35), residues: 562 helix: -0.26 (0.40), residues: 181 sheet: 0.18 (0.53), residues: 110 loop : -2.35 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 68 HIS 0.004 0.001 HIS C 398 PHE 0.018 0.001 PHE D 9 TYR 0.021 0.002 TYR C 225 ARG 0.012 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 135) hydrogen bonds : angle 5.80032 ( 366) covalent geometry : bond 0.00342 ( 4533) covalent geometry : angle 0.69686 ( 6131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.514 Fit side-chains REVERT: C 226 ASN cc_start: 0.8068 (m-40) cc_final: 0.7137 (t0) REVERT: C 375 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8074 (tt) REVERT: D 7 SER cc_start: 0.7388 (OUTLIER) cc_final: 0.6913 (p) REVERT: D 19 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7563 (t0) outliers start: 26 outliers final: 22 residues processed: 103 average time/residue: 0.1577 time to fit residues: 20.8803 Evaluate side-chains 104 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.191995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153078 restraints weight = 5488.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156313 restraints weight = 4522.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157679 restraints weight = 3287.526| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4533 Z= 0.154 Angle : 0.703 12.635 6131 Z= 0.357 Chirality : 0.048 0.187 708 Planarity : 0.004 0.047 793 Dihedral : 5.136 23.481 600 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.72 % Favored : 91.10 % Rotamer: Outliers : 5.22 % Allowed : 30.52 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.35), residues: 562 helix: -0.25 (0.40), residues: 181 sheet: 0.11 (0.52), residues: 110 loop : -2.33 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 68 HIS 0.004 0.001 HIS E 16 PHE 0.017 0.001 PHE D 9 TYR 0.022 0.002 TYR C 225 ARG 0.011 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 135) hydrogen bonds : angle 5.81375 ( 366) covalent geometry : bond 0.00366 ( 4533) covalent geometry : angle 0.70253 ( 6131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: C 226 ASN cc_start: 0.8095 (m-40) cc_final: 0.7147 (t0) REVERT: C 375 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8122 (tt) REVERT: C 394 MET cc_start: 0.8065 (mmm) cc_final: 0.7535 (mmm) REVERT: D 7 SER cc_start: 0.7446 (OUTLIER) cc_final: 0.6963 (p) REVERT: D 19 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7615 (t0) REVERT: D 44 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7330 (mtp85) outliers start: 26 outliers final: 22 residues processed: 104 average time/residue: 0.1771 time to fit residues: 22.9464 Evaluate side-chains 107 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 HIS ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135140 restraints weight = 5401.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137961 restraints weight = 4966.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138560 restraints weight = 3688.277| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4533 Z= 0.171 Angle : 0.715 12.621 6131 Z= 0.364 Chirality : 0.049 0.174 708 Planarity : 0.004 0.045 793 Dihedral : 5.177 23.405 600 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.90 % Favored : 90.93 % Rotamer: Outliers : 5.42 % Allowed : 30.12 % Favored : 64.46 % 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: -1.68 (0.35), residues: 562 helix: -0.27 (0.40), residues: 179 sheet: 0.01 (0.52), residues: 110 loop : -2.22 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 68 HIS 0.005 0.001 HIS E 16 PHE 0.016 0.002 PHE D 9 TYR 0.022 0.002 TYR C 225 ARG 0.010 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 135) hydrogen bonds : angle 5.87260 ( 366) covalent geometry : bond 0.00406 ( 4533) covalent geometry : angle 0.71549 ( 6131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.01 seconds wall clock time: 33 minutes 58.80 seconds (2038.80 seconds total)