Starting phenix.real_space_refine on Thu Nov 14 06:32:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_42049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_42049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_42049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_42049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua3_42049/11_2024/8ua3_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-5513/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: 4.15, per 1000 atoms: 0.93 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: 1.10 Conformation dependent library (CDL) restraints added in 565.2 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: 0.70 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: 1.26 Time building geometry restraints manager: 1.29 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.580 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- 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= 0.303 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 *********************** 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 : 0.479 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: 0.1755 time to fit residues: 26.0831 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 : 0.561 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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= 0.234 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 *********************** 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 : 0.466 Fit side-chains revert: symmetry clash REVERT: C 129 MET cc_start: 0.6334 (mpp) cc_final: 0.5383 (ttm) REVERT: C 343 ASP cc_start: 0.7329 (t0) cc_final: 0.7118 (m-30) REVERT: C 347 LYS cc_start: 0.7559 (tptm) cc_final: 0.6992 (tttp) REVERT: E 41 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7240 (tp30) REVERT: E 44 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8193 (mtp85) outliers start: 20 outliers final: 12 residues processed: 102 average time/residue: 0.1482 time to fit residues: 19.6604 Evaluate side-chains 92 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4533 Z= 0.203 Angle : 0.646 10.139 6131 Z= 0.339 Chirality : 0.047 0.143 708 Planarity : 0.004 0.037 793 Dihedral : 5.331 24.344 600 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.83 % Favored : 91.81 % Rotamer: Outliers : 4.22 % Allowed : 29.92 % 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: -2.01 (0.35), residues: 562 helix: -0.80 (0.40), residues: 182 sheet: 0.18 (0.54), residues: 113 loop : -2.45 (0.35), residues: 267 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 0.013 0.001 PHE E 112 TYR 0.007 0.001 TYR E 11 ARG 0.007 0.000 ARG C 335 *********************** 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 103 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 129 MET cc_start: 0.6255 (mpp) cc_final: 0.5348 (ttm) REVERT: C 347 LYS cc_start: 0.7585 (tptm) cc_final: 0.7274 (tttp) REVERT: E 44 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8144 (mtp85) REVERT: E 105 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7811 (tp30) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.1558 time to fit residues: 19.0613 Evaluate side-chains 92 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 158 MET 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 26 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4533 Z= 0.445 Angle : 0.782 12.749 6131 Z= 0.410 Chirality : 0.052 0.157 708 Planarity : 0.004 0.043 793 Dihedral : 5.902 23.716 600 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.25 % Favored : 90.39 % Rotamer: Outliers : 7.03 % Allowed : 28.11 % Favored : 64.86 % 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: -2.29 (0.35), residues: 562 helix: -1.06 (0.39), residues: 176 sheet: -0.29 (0.54), residues: 113 loop : -2.40 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 68 HIS 0.008 0.002 HIS C 398 PHE 0.017 0.002 PHE D 112 TYR 0.017 0.002 TYR E 11 ARG 0.009 0.001 ARG C 335 *********************** 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 115 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.516 Fit side-chains REVERT: C 226 ASN cc_start: 0.8118 (m-40) cc_final: 0.7128 (t0) REVERT: C 269 ASP cc_start: 0.7903 (t0) cc_final: 0.7667 (t0) REVERT: C 343 ASP cc_start: 0.7632 (t0) cc_final: 0.7247 (m-30) REVERT: E 44 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8221 (mtp85) REVERT: E 105 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7880 (tp30) outliers start: 35 outliers final: 23 residues processed: 106 average time/residue: 0.1803 time to fit residues: 23.8995 Evaluate side-chains 98 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 391 THR 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 79 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 117 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4533 Z= 0.218 Angle : 0.663 13.179 6131 Z= 0.343 Chirality : 0.048 0.143 708 Planarity : 0.004 0.044 793 Dihedral : 5.439 24.144 600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.01 % Favored : 91.81 % Rotamer: Outliers : 5.62 % Allowed : 29.32 % Favored : 65.06 % 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: -2.02 (0.36), residues: 562 helix: -0.75 (0.39), residues: 181 sheet: -0.34 (0.54), residues: 115 loop : -2.24 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 68 HIS 0.004 0.001 HIS C 398 PHE 0.025 0.002 PHE D 9 TYR 0.019 0.002 TYR C 225 ARG 0.008 0.001 ARG C 335 *********************** 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 116 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.499 Fit side-chains REVERT: C 226 ASN cc_start: 0.8145 (m-40) cc_final: 0.7047 (t0) REVERT: C 343 ASP cc_start: 0.7368 (t0) cc_final: 0.7147 (m-30) REVERT: C 375 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7616 (tt) REVERT: E 44 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8230 (mtp85) REVERT: E 77 GLU cc_start: 0.7235 (pm20) cc_final: 0.6991 (pm20) REVERT: E 81 VAL cc_start: 0.8407 (m) cc_final: 0.8152 (t) REVERT: E 105 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7953 (tp30) outliers start: 28 outliers final: 20 residues processed: 107 average time/residue: 0.1602 time to fit residues: 21.9547 Evaluate side-chains 103 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 ASN 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 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 57 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4533 Z= 0.223 Angle : 0.677 15.057 6131 Z= 0.343 Chirality : 0.047 0.142 708 Planarity : 0.004 0.047 793 Dihedral : 5.346 24.079 600 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.90 % Favored : 90.93 % Rotamer: Outliers : 5.42 % Allowed : 30.52 % Favored : 64.06 % 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: -1.94 (0.36), residues: 562 helix: -0.60 (0.40), residues: 181 sheet: -0.41 (0.52), residues: 115 loop : -2.20 (0.36), residues: 266 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 0.015 0.001 PHE C 355 TYR 0.019 0.002 TYR C 225 ARG 0.010 0.001 ARG C 335 *********************** 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 109 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.463 Fit side-chains REVERT: C 226 ASN cc_start: 0.8138 (m-40) cc_final: 0.7062 (t0) REVERT: C 343 ASP cc_start: 0.7410 (t0) cc_final: 0.7193 (m-30) REVERT: C 375 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7600 (tt) REVERT: D 105 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7867 (mm-30) REVERT: E 44 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8246 (mtp85) REVERT: E 77 GLU cc_start: 0.7293 (pm20) cc_final: 0.6968 (pm20) REVERT: E 105 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7964 (tp30) outliers start: 27 outliers final: 21 residues processed: 103 average time/residue: 0.1670 time to fit residues: 21.8320 Evaluate side-chains 100 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 ASN 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 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 57 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0020 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN E 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4533 Z= 0.169 Angle : 0.649 13.583 6131 Z= 0.328 Chirality : 0.047 0.158 708 Planarity : 0.003 0.044 793 Dihedral : 5.146 24.176 600 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.53 % Rotamer: Outliers : 3.41 % Allowed : 32.13 % 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: -1.78 (0.36), residues: 562 helix: -0.37 (0.41), residues: 181 sheet: -0.11 (0.53), residues: 112 loop : -2.27 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 68 HIS 0.003 0.001 HIS C 398 PHE 0.018 0.001 PHE D 9 TYR 0.019 0.001 TYR C 225 ARG 0.011 0.001 ARG C 335 *********************** 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: 17 poor density : 96 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: C 226 ASN cc_start: 0.8052 (m-40) cc_final: 0.6885 (t0) REVERT: C 343 ASP cc_start: 0.7296 (t0) cc_final: 0.7080 (m-30) REVERT: C 375 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7551 (tt) REVERT: E 22 LEU cc_start: 0.8756 (mm) cc_final: 0.8530 (mm) REVERT: E 105 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7979 (tp30) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.1535 time to fit residues: 21.0652 Evaluate side-chains 98 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 375 LEU Chi-restraints excluded: chain D residue 37 THR 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 51 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3077 > 50: distance: 37 - 44: 35.117 distance: 44 - 45: 56.531 distance: 44 - 195: 32.035 distance: 45 - 46: 57.593 distance: 45 - 48: 41.266 distance: 46 - 47: 68.108 distance: 46 - 52: 70.245 distance: 47 - 192: 37.445 distance: 48 - 50: 39.765 distance: 49 - 51: 55.305 distance: 52 - 53: 57.092 distance: 53 - 54: 40.727 distance: 53 - 56: 55.575 distance: 54 - 60: 56.754 distance: 56 - 57: 47.484 distance: 57 - 58: 46.427 distance: 57 - 59: 47.239 distance: 60 - 61: 48.767 distance: 61 - 62: 42.267 distance: 61 - 64: 46.648 distance: 62 - 71: 56.886 distance: 64 - 65: 39.052 distance: 66 - 67: 39.746 distance: 68 - 70: 40.404 distance: 71 - 72: 40.417 distance: 72 - 73: 38.478 distance: 72 - 75: 41.388 distance: 73 - 74: 40.655 distance: 73 - 80: 69.480 distance: 75 - 76: 55.590 distance: 76 - 77: 55.064 distance: 77 - 78: 39.758 distance: 78 - 79: 55.940 distance: 80 - 81: 4.864 distance: 81 - 82: 39.339 distance: 81 - 84: 53.383 distance: 82 - 86: 57.358 distance: 86 - 87: 39.296 distance: 87 - 88: 41.133 distance: 87 - 90: 57.625 distance: 88 - 94: 55.357 distance: 91 - 92: 69.923 distance: 91 - 93: 55.336 distance: 94 - 95: 57.779 distance: 95 - 96: 39.300 distance: 96 - 97: 56.741 distance: 98 - 99: 39.086 distance: 99 - 100: 39.415 distance: 103 - 104: 57.930 distance: 104 - 105: 55.195 distance: 104 - 107: 57.922 distance: 105 - 106: 57.536 distance: 105 - 110: 56.713 distance: 107 - 108: 47.330 distance: 107 - 109: 12.958 distance: 110 - 111: 40.157 distance: 111 - 112: 40.209 distance: 111 - 114: 39.722 distance: 112 - 113: 55.555 distance: 112 - 119: 56.604 distance: 114 - 115: 41.466 distance: 115 - 116: 39.226 distance: 117 - 118: 56.370 distance: 119 - 120: 8.319 distance: 120 - 121: 7.764 distance: 120 - 123: 5.874 distance: 121 - 122: 57.770 distance: 121 - 127: 34.245 distance: 123 - 124: 57.624