Starting phenix.real_space_refine on Fri Oct 11 21:44:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq9_38570/10_2024/8xq9_38570.cif" } resolution = 3.77 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= 0.002 sd= 0.032 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 60 5.16 5 C 6976 2.51 5 N 1766 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5336 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Chain: "B" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5336 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Time building chain proxies: 7.76, per 1000 atoms: 0.73 Number of scatterers: 10672 At special positions: 0 Unit cell: (102.6, 115.56, 115.56, 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 60 16.00 O 1870 8.00 N 1766 7.00 C 6976 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.943A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.854A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 413 Proline residue: A 408 - end of helix removed outlier: 3.889A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.986A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.285A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.655A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 573 through 601 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.034A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 853 Processing helix chain 'A' and resid 853 through 858 removed outlier: 4.335A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'B' and resid 76 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.028A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 134 through 153 removed outlier: 3.592A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.847A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 removed outlier: 3.900A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 4.230A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 432 through 445 Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.438A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.910A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 573 through 600 Processing helix chain 'B' and resid 604 through 620 Processing helix chain 'B' and resid 639 through 653 removed outlier: 3.893A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 853 removed outlier: 3.809A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 4.228A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.537A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 918 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.577A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2715 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: 3.86 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3357 1.34 - 1.46: 2018 1.46 - 1.58: 5393 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10880 Sorted by residual: bond pdb=" CA PRO B 949 " pdb=" C PRO B 949 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.43e+00 bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.20e+00 bond pdb=" CA ILE A 488 " pdb=" C ILE A 488 " ideal model delta sigma weight residual 1.520 1.536 -0.016 8.80e-03 1.29e+04 3.29e+00 bond pdb=" C ILE B 818 " pdb=" N PRO B 819 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.79e+00 bond pdb=" C LEU B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.71e+00 ... (remaining 10875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 14447 2.02 - 4.05: 273 4.05 - 6.07: 18 6.07 - 8.09: 17 8.09 - 10.11: 7 Bond angle restraints: 14762 Sorted by residual: angle pdb=" C GLU A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta sigma weight residual 126.32 134.30 -7.98 1.74e+00 3.30e-01 2.10e+01 angle pdb=" C PHE A 294 " pdb=" N ASN A 295 " pdb=" CA ASN A 295 " ideal model delta sigma weight residual 122.08 128.75 -6.67 1.47e+00 4.63e-01 2.06e+01 angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 123.07 -2.83 6.30e-01 2.52e+00 2.02e+01 angle pdb=" C GLU B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta sigma weight residual 126.32 133.64 -7.32 1.74e+00 3.30e-01 1.77e+01 angle pdb=" C SER B 487 " pdb=" N ILE B 488 " pdb=" CA ILE B 488 " ideal model delta sigma weight residual 120.33 123.35 -3.02 8.00e-01 1.56e+00 1.43e+01 ... (remaining 14757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5903 17.58 - 35.16: 431 35.16 - 52.74: 147 52.74 - 70.32: 22 70.32 - 87.90: 3 Dihedral angle restraints: 6506 sinusoidal: 2554 harmonic: 3952 Sorted by residual: dihedral pdb=" CA GLU A 337 " pdb=" C GLU A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta harmonic sigma weight residual -180.00 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA LYS B 338 " pdb=" C LYS B 338 " pdb=" N THR B 339 " pdb=" CA THR B 339 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" N THR A 339 " pdb=" CA THR A 339 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 6503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1323 0.047 - 0.093: 358 0.093 - 0.140: 91 0.140 - 0.186: 9 0.186 - 0.233: 1 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB ILE A 488 " pdb=" CA ILE A 488 " pdb=" CG1 ILE A 488 " pdb=" CG2 ILE A 488 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN A 295 " pdb=" N ASN A 295 " pdb=" C ASN A 295 " pdb=" CB ASN A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA SER B 407 " pdb=" N SER B 407 " pdb=" C SER B 407 " pdb=" CB SER B 407 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1779 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 818 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 819 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 819 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 819 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C LEU B 467 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU B 467 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 468 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 271 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C VAL A 271 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL A 271 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 272 " 0.010 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2922 2.81 - 3.34: 10555 3.34 - 3.86: 18370 3.86 - 4.38: 19514 4.38 - 4.90: 34749 Nonbonded interactions: 86110 Sorted by model distance: nonbonded pdb=" OD1 ASN A 194 " pdb=" OG SER A 196 " model vdw 2.293 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.298 3.040 nonbonded pdb=" O ILE B 462 " pdb=" OG1 THR B 466 " model vdw 2.309 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASN B 194 " pdb=" OG SER B 196 " model vdw 2.334 3.040 ... (remaining 86105 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.340 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.003 0.059 10880 Z= 0.209 Angle : 0.712 10.113 14762 Z= 0.393 Chirality : 0.045 0.233 1782 Planarity : 0.006 0.055 1816 Dihedral : 14.170 87.897 3946 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.48 % Allowed : 11.29 % Favored : 84.22 % 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: -1.10 (0.20), residues: 1354 helix: -0.46 (0.13), residues: 1138 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 643 HIS 0.002 0.000 HIS A 350 PHE 0.011 0.001 PHE B 455 TYR 0.012 0.001 TYR B 392 ARG 0.002 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 474 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8031 (mt) cc_final: 0.7609 (mm) REVERT: A 112 ILE cc_start: 0.8065 (mt) cc_final: 0.7770 (mt) REVERT: A 113 LEU cc_start: 0.8152 (tt) cc_final: 0.7861 (tp) REVERT: A 124 GLU cc_start: 0.6952 (tt0) cc_final: 0.6404 (tt0) REVERT: A 134 ASP cc_start: 0.8102 (t70) cc_final: 0.7716 (t0) REVERT: A 155 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6543 (p0) REVERT: A 158 THR cc_start: 0.8144 (m) cc_final: 0.7574 (p) REVERT: A 180 LEU cc_start: 0.8496 (mt) cc_final: 0.8215 (mm) REVERT: A 197 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 199 MET cc_start: 0.7636 (tpt) cc_final: 0.7416 (tpt) REVERT: A 204 ILE cc_start: 0.8625 (mt) cc_final: 0.8342 (tt) REVERT: A 211 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7890 (p) REVERT: A 216 LEU cc_start: 0.8573 (mp) cc_final: 0.8325 (mp) REVERT: A 226 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 233 GLU cc_start: 0.7841 (tt0) cc_final: 0.6421 (tt0) REVERT: A 234 SER cc_start: 0.7897 (p) cc_final: 0.7276 (p) REVERT: A 236 LEU cc_start: 0.8257 (mt) cc_final: 0.7979 (mp) REVERT: A 237 ASN cc_start: 0.8115 (t0) cc_final: 0.7561 (t0) REVERT: A 238 ASP cc_start: 0.7323 (m-30) cc_final: 0.6890 (m-30) REVERT: A 240 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 248 PHE cc_start: 0.8077 (m-80) cc_final: 0.7526 (m-10) REVERT: A 251 MET cc_start: 0.7609 (ttm) cc_final: 0.7241 (ttm) REVERT: A 294 PHE cc_start: 0.7990 (m-80) cc_final: 0.7724 (m-80) REVERT: A 312 TYR cc_start: 0.8166 (t80) cc_final: 0.7784 (t80) REVERT: A 316 ASP cc_start: 0.7348 (m-30) cc_final: 0.6962 (m-30) REVERT: A 350 HIS cc_start: 0.8552 (m-70) cc_final: 0.7938 (m90) REVERT: A 351 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7888 (tpp80) REVERT: A 364 ILE cc_start: 0.8197 (mt) cc_final: 0.7791 (mt) REVERT: A 384 ASP cc_start: 0.8037 (t0) cc_final: 0.7718 (t0) REVERT: A 393 LEU cc_start: 0.8772 (mp) cc_final: 0.8463 (mp) REVERT: A 396 THR cc_start: 0.8366 (m) cc_final: 0.8097 (p) REVERT: A 399 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7489 (tpt170) REVERT: A 401 MET cc_start: 0.7685 (ttm) cc_final: 0.7399 (ttm) REVERT: A 427 TRP cc_start: 0.8403 (t-100) cc_final: 0.8152 (t-100) REVERT: A 443 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 444 ASN cc_start: 0.8440 (t0) cc_final: 0.8114 (t0) REVERT: A 445 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 465 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 480 ILE cc_start: 0.8475 (mt) cc_final: 0.8138 (mm) REVERT: A 485 ASP cc_start: 0.8121 (t0) cc_final: 0.7764 (t0) REVERT: A 499 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7753 (ttp80) REVERT: A 502 HIS cc_start: 0.8042 (t70) cc_final: 0.7529 (t70) REVERT: A 505 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 506 ASN cc_start: 0.8401 (m-40) cc_final: 0.7848 (m-40) REVERT: A 507 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7881 (ptp-110) REVERT: A 511 MET cc_start: 0.8154 (ttm) cc_final: 0.7409 (tmm) REVERT: A 533 SER cc_start: 0.8522 (p) cc_final: 0.8223 (p) REVERT: A 534 ASP cc_start: 0.7617 (t0) cc_final: 0.7384 (t0) REVERT: A 586 MET cc_start: 0.7756 (ptm) cc_final: 0.7304 (ptm) REVERT: A 587 LEU cc_start: 0.8808 (pp) cc_final: 0.8487 (pp) REVERT: A 590 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 591 LYS cc_start: 0.8759 (pttp) cc_final: 0.8498 (pttp) REVERT: A 610 LEU cc_start: 0.8873 (tt) cc_final: 0.8038 (tp) REVERT: A 613 GLN cc_start: 0.8428 (pp30) cc_final: 0.7866 (pp30) REVERT: A 832 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 833 LEU cc_start: 0.8859 (tp) cc_final: 0.8599 (mm) REVERT: A 844 ILE cc_start: 0.9028 (mm) cc_final: 0.8392 (pt) REVERT: A 848 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 875 ARG cc_start: 0.7513 (ttp80) cc_final: 0.6827 (ttp80) REVERT: A 897 LYS cc_start: 0.8724 (pttt) cc_final: 0.8509 (pttt) REVERT: A 899 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7382 (mtt90) REVERT: A 900 GLN cc_start: 0.8128 (tt0) cc_final: 0.7886 (tt0) REVERT: A 906 LEU cc_start: 0.8474 (mt) cc_final: 0.8092 (mm) REVERT: A 909 SER cc_start: 0.8696 (t) cc_final: 0.8153 (p) REVERT: A 911 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 938 MET cc_start: 0.8282 (tpp) cc_final: 0.7877 (tpp) REVERT: B 90 ILE cc_start: 0.8238 (mt) cc_final: 0.7956 (mm) REVERT: B 118 SER cc_start: 0.8190 (t) cc_final: 0.7778 (p) REVERT: B 155 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6266 (p0) REVERT: B 161 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7653 (ptp-170) REVERT: B 162 SER cc_start: 0.8908 (t) cc_final: 0.8578 (t) REVERT: B 163 PHE cc_start: 0.7970 (t80) cc_final: 0.7739 (t80) REVERT: B 165 GLN cc_start: 0.8177 (pt0) cc_final: 0.7899 (pt0) REVERT: B 166 VAL cc_start: 0.8682 (t) cc_final: 0.8367 (p) REVERT: B 189 PHE cc_start: 0.7893 (m-10) cc_final: 0.7402 (m-10) REVERT: B 191 TYR cc_start: 0.8355 (m-80) cc_final: 0.7953 (m-80) REVERT: B 199 MET cc_start: 0.7330 (tpt) cc_final: 0.6810 (tpp) REVERT: B 218 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8054 (ptmm) REVERT: B 237 ASN cc_start: 0.8049 (t0) cc_final: 0.7593 (t0) REVERT: B 248 PHE cc_start: 0.8077 (m-80) cc_final: 0.7349 (m-80) REVERT: B 249 MET cc_start: 0.7658 (tmm) cc_final: 0.7311 (tmm) REVERT: B 251 MET cc_start: 0.6824 (tmm) cc_final: 0.6474 (tmm) REVERT: B 263 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 280 TYR cc_start: 0.7621 (t80) cc_final: 0.7133 (t80) REVERT: B 293 ILE cc_start: 0.8354 (mt) cc_final: 0.8124 (tp) REVERT: B 319 LEU cc_start: 0.7447 (mp) cc_final: 0.7239 (mt) REVERT: B 321 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6298 (t) REVERT: B 335 ASN cc_start: 0.8419 (t0) cc_final: 0.8007 (t0) REVERT: B 339 THR cc_start: 0.8536 (p) cc_final: 0.8168 (p) REVERT: B 344 GLU cc_start: 0.7382 (pp20) cc_final: 0.7084 (pp20) REVERT: B 375 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7855 (ptpt) REVERT: B 377 LEU cc_start: 0.7622 (tp) cc_final: 0.7209 (tp) REVERT: B 383 MET cc_start: 0.7236 (tpp) cc_final: 0.5881 (tpp) REVERT: B 387 TYR cc_start: 0.7576 (m-10) cc_final: 0.7242 (m-80) REVERT: B 388 LEU cc_start: 0.8542 (tt) cc_final: 0.8305 (tp) REVERT: B 397 ILE cc_start: 0.8376 (mt) cc_final: 0.7445 (mm) REVERT: B 401 MET cc_start: 0.7735 (mtp) cc_final: 0.7094 (mtp) REVERT: B 413 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6276 (pt) REVERT: B 418 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 424 ILE cc_start: 0.8824 (tp) cc_final: 0.8621 (tp) REVERT: B 444 ASN cc_start: 0.8074 (t0) cc_final: 0.7865 (t0) REVERT: B 445 LEU cc_start: 0.8423 (tp) cc_final: 0.8139 (tp) REVERT: B 466 THR cc_start: 0.7743 (p) cc_final: 0.7491 (t) REVERT: B 470 ASN cc_start: 0.7791 (m-40) cc_final: 0.7447 (m110) REVERT: B 475 GLN cc_start: 0.8153 (tp40) cc_final: 0.7845 (tp40) REVERT: B 477 LEU cc_start: 0.8633 (mp) cc_final: 0.8206 (tp) REVERT: B 480 ILE cc_start: 0.7991 (mt) cc_final: 0.7789 (mt) REVERT: B 481 LEU cc_start: 0.8619 (mt) cc_final: 0.8075 (mm) REVERT: B 494 MET cc_start: 0.7574 (tpp) cc_final: 0.7159 (tpp) REVERT: B 500 ARG cc_start: 0.7861 (tmt-80) cc_final: 0.7477 (ttt-90) REVERT: B 512 LEU cc_start: 0.8777 (mp) cc_final: 0.8365 (mt) REVERT: B 517 PHE cc_start: 0.7302 (m-80) cc_final: 0.7086 (m-10) REVERT: B 580 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6654 (tp30) REVERT: B 583 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6485 (ttp-110) REVERT: B 586 MET cc_start: 0.7561 (tpt) cc_final: 0.7181 (tpt) REVERT: B 590 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 594 TYR cc_start: 0.8205 (m-10) cc_final: 0.8004 (m-80) REVERT: B 598 PHE cc_start: 0.8264 (t80) cc_final: 0.7797 (t80) REVERT: B 826 ASN cc_start: 0.8083 (t0) cc_final: 0.7166 (t0) REVERT: B 830 ASN cc_start: 0.8305 (m-40) cc_final: 0.7826 (m110) REVERT: B 832 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 848 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7861 (mm-30) REVERT: B 877 GLN cc_start: 0.8184 (pp30) cc_final: 0.7709 (pp30) REVERT: B 880 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7813 (ptpp) REVERT: B 881 GLU cc_start: 0.7745 (pt0) cc_final: 0.7456 (pt0) REVERT: B 885 LEU cc_start: 0.8385 (tp) cc_final: 0.8154 (tp) REVERT: B 889 HIS cc_start: 0.7445 (m-70) cc_final: 0.6946 (m-70) REVERT: B 899 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.6689 (tmm-80) REVERT: B 902 ILE cc_start: 0.8903 (tt) cc_final: 0.8552 (tp) REVERT: B 903 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7798 (ttm170) REVERT: B 921 LEU cc_start: 0.8762 (tt) cc_final: 0.8284 (mm) outliers start: 52 outliers final: 14 residues processed: 500 average time/residue: 0.2636 time to fit residues: 176.9570 Evaluate side-chains 478 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 453 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 264 ASN A 295 ASN A 374 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 421 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10880 Z= 0.239 Angle : 0.627 9.866 14762 Z= 0.336 Chirality : 0.040 0.218 1782 Planarity : 0.005 0.045 1816 Dihedral : 7.206 57.890 1499 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.14 % Allowed : 18.79 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1354 helix: 1.05 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 635 HIS 0.004 0.001 HIS A 600 PHE 0.021 0.001 PHE A 598 TYR 0.016 0.001 TYR B 837 ARG 0.006 0.001 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 468 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8098 (mt) cc_final: 0.7767 (mm) REVERT: A 113 LEU cc_start: 0.8245 (tt) cc_final: 0.8010 (tp) REVERT: A 134 ASP cc_start: 0.7848 (t70) cc_final: 0.7556 (t0) REVERT: A 155 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6115 (p0) REVERT: A 158 THR cc_start: 0.8310 (m) cc_final: 0.7576 (p) REVERT: A 161 ARG cc_start: 0.7576 (mmt180) cc_final: 0.7111 (mmt180) REVERT: A 191 TYR cc_start: 0.8257 (m-80) cc_final: 0.7788 (m-80) REVERT: A 204 ILE cc_start: 0.8698 (mt) cc_final: 0.8367 (tt) REVERT: A 205 MET cc_start: 0.7855 (mmp) cc_final: 0.7551 (tpp) REVERT: A 206 SER cc_start: 0.8264 (t) cc_final: 0.7782 (p) REVERT: A 211 VAL cc_start: 0.8107 (m) cc_final: 0.7881 (p) REVERT: A 233 GLU cc_start: 0.8121 (tt0) cc_final: 0.7905 (tt0) REVERT: A 234 SER cc_start: 0.8107 (p) cc_final: 0.7341 (p) REVERT: A 238 ASP cc_start: 0.7327 (m-30) cc_final: 0.6832 (m-30) REVERT: A 248 PHE cc_start: 0.8077 (m-80) cc_final: 0.7429 (m-10) REVERT: A 251 MET cc_start: 0.7696 (ttm) cc_final: 0.7288 (ttm) REVERT: A 252 VAL cc_start: 0.7275 (t) cc_final: 0.6538 (m) REVERT: A 294 PHE cc_start: 0.8086 (m-80) cc_final: 0.7797 (m-80) REVERT: A 312 TYR cc_start: 0.8271 (t80) cc_final: 0.7692 (t80) REVERT: A 316 ASP cc_start: 0.7431 (m-30) cc_final: 0.6939 (m-30) REVERT: A 351 ARG cc_start: 0.8218 (tpp80) cc_final: 0.7945 (tpp80) REVERT: A 364 ILE cc_start: 0.8092 (mt) cc_final: 0.7596 (tt) REVERT: A 384 ASP cc_start: 0.8192 (t0) cc_final: 0.7940 (t0) REVERT: A 393 LEU cc_start: 0.8864 (mp) cc_final: 0.8432 (mp) REVERT: A 396 THR cc_start: 0.8353 (m) cc_final: 0.8092 (p) REVERT: A 401 MET cc_start: 0.7761 (ttm) cc_final: 0.7541 (ttm) REVERT: A 425 MET cc_start: 0.7831 (tpt) cc_final: 0.7607 (tpt) REVERT: A 443 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 466 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7894 (t) REVERT: A 485 ASP cc_start: 0.8104 (t0) cc_final: 0.7728 (t0) REVERT: A 494 MET cc_start: 0.8210 (tpp) cc_final: 0.7821 (tpp) REVERT: A 499 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7850 (ttp80) REVERT: A 500 ARG cc_start: 0.8253 (ttt90) cc_final: 0.7906 (ttt180) REVERT: A 501 ILE cc_start: 0.8674 (tt) cc_final: 0.8428 (pt) REVERT: A 502 HIS cc_start: 0.8203 (t70) cc_final: 0.7778 (t70) REVERT: A 505 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 506 ASN cc_start: 0.8526 (m-40) cc_final: 0.7935 (m110) REVERT: A 507 ARG cc_start: 0.8159 (ptp-110) cc_final: 0.7873 (ptp-110) REVERT: A 533 SER cc_start: 0.8739 (p) cc_final: 0.8460 (p) REVERT: A 534 ASP cc_start: 0.7924 (t0) cc_final: 0.7561 (t0) REVERT: A 579 MET cc_start: 0.7175 (mmm) cc_final: 0.6812 (tpt) REVERT: A 585 ARG cc_start: 0.8479 (tmm-80) cc_final: 0.8277 (tmm-80) REVERT: A 586 MET cc_start: 0.7815 (ptm) cc_final: 0.7361 (ptm) REVERT: A 587 LEU cc_start: 0.8883 (pp) cc_final: 0.8600 (pp) REVERT: A 590 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8100 (mt-10) REVERT: A 591 LYS cc_start: 0.8740 (pttp) cc_final: 0.8525 (pttp) REVERT: A 600 HIS cc_start: 0.7945 (t70) cc_final: 0.7622 (t70) REVERT: A 610 LEU cc_start: 0.8862 (tt) cc_final: 0.8090 (tp) REVERT: A 613 GLN cc_start: 0.8511 (pp30) cc_final: 0.7869 (pp30) REVERT: A 830 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7899 (t0) REVERT: A 832 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 833 LEU cc_start: 0.8838 (tp) cc_final: 0.8636 (mm) REVERT: A 844 ILE cc_start: 0.9029 (mm) cc_final: 0.8312 (tt) REVERT: A 848 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 875 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7235 (ttp80) REVERT: A 887 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7299 (mtm110) REVERT: A 888 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 897 LYS cc_start: 0.8690 (pttt) cc_final: 0.8487 (pttt) REVERT: A 899 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7401 (mtt90) REVERT: A 906 LEU cc_start: 0.8442 (mt) cc_final: 0.8128 (mm) REVERT: A 909 SER cc_start: 0.8713 (t) cc_final: 0.8480 (p) REVERT: A 911 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 923 ASP cc_start: 0.5298 (p0) cc_final: 0.4938 (p0) REVERT: A 926 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 931 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7807 (mt-10) REVERT: B 78 ILE cc_start: 0.8089 (tt) cc_final: 0.7594 (mt) REVERT: B 90 ILE cc_start: 0.8240 (mt) cc_final: 0.7934 (mm) REVERT: B 92 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8301 (mmm-85) REVERT: B 118 SER cc_start: 0.8438 (t) cc_final: 0.8186 (p) REVERT: B 156 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8325 (t) REVERT: B 163 PHE cc_start: 0.8100 (t80) cc_final: 0.7611 (t80) REVERT: B 166 VAL cc_start: 0.8457 (t) cc_final: 0.8189 (p) REVERT: B 186 MET cc_start: 0.7775 (mmm) cc_final: 0.7442 (mmm) REVERT: B 189 PHE cc_start: 0.7936 (m-10) cc_final: 0.7549 (m-10) REVERT: B 194 ASN cc_start: 0.7648 (p0) cc_final: 0.7436 (p0) REVERT: B 197 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: B 199 MET cc_start: 0.7438 (tpt) cc_final: 0.7210 (tpp) REVERT: B 218 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8227 (ptmm) REVERT: B 225 GLN cc_start: 0.7442 (pm20) cc_final: 0.7237 (pm20) REVERT: B 237 ASN cc_start: 0.8001 (t0) cc_final: 0.7580 (t0) REVERT: B 242 ILE cc_start: 0.8506 (mt) cc_final: 0.8189 (mm) REVERT: B 248 PHE cc_start: 0.8066 (m-80) cc_final: 0.7364 (m-80) REVERT: B 251 MET cc_start: 0.6935 (tmm) cc_final: 0.6543 (tmm) REVERT: B 263 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 293 ILE cc_start: 0.8399 (mt) cc_final: 0.8189 (tp) REVERT: B 321 VAL cc_start: 0.6991 (OUTLIER) cc_final: 0.6768 (t) REVERT: B 335 ASN cc_start: 0.8225 (t0) cc_final: 0.7938 (t0) REVERT: B 338 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7491 (ptpt) REVERT: B 344 GLU cc_start: 0.7572 (pp20) cc_final: 0.7327 (pp20) REVERT: B 375 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7836 (ptpt) REVERT: B 383 MET cc_start: 0.7153 (tpp) cc_final: 0.5965 (tpp) REVERT: B 387 TYR cc_start: 0.7764 (m-10) cc_final: 0.7378 (m-80) REVERT: B 393 LEU cc_start: 0.8582 (mp) cc_final: 0.8344 (mp) REVERT: B 397 ILE cc_start: 0.8557 (mt) cc_final: 0.7675 (mm) REVERT: B 399 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8544 (ttt90) REVERT: B 401 MET cc_start: 0.7941 (mtp) cc_final: 0.7274 (mtp) REVERT: B 406 PHE cc_start: 0.8217 (m-80) cc_final: 0.7908 (m-80) REVERT: B 424 ILE cc_start: 0.8833 (tp) cc_final: 0.8596 (tp) REVERT: B 425 MET cc_start: 0.8287 (mtt) cc_final: 0.8050 (mtp) REVERT: B 444 ASN cc_start: 0.8041 (t0) cc_final: 0.7769 (t0) REVERT: B 445 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8132 (tp) REVERT: B 457 PHE cc_start: 0.8588 (t80) cc_final: 0.8355 (t80) REVERT: B 458 HIS cc_start: 0.8598 (m-70) cc_final: 0.8384 (m-70) REVERT: B 466 THR cc_start: 0.7640 (p) cc_final: 0.7359 (t) REVERT: B 470 ASN cc_start: 0.7634 (m-40) cc_final: 0.7364 (m110) REVERT: B 477 LEU cc_start: 0.8656 (mp) cc_final: 0.8259 (tp) REVERT: B 480 ILE cc_start: 0.8119 (mt) cc_final: 0.7880 (mt) REVERT: B 490 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8570 (ttmt) REVERT: B 494 MET cc_start: 0.7552 (tpp) cc_final: 0.7315 (tpp) REVERT: B 500 ARG cc_start: 0.8006 (tmt-80) cc_final: 0.7590 (ttt-90) REVERT: B 512 LEU cc_start: 0.8899 (mp) cc_final: 0.8467 (mm) REVERT: B 580 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7191 (tp30) REVERT: B 586 MET cc_start: 0.7730 (tpt) cc_final: 0.7337 (tpt) REVERT: B 590 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 594 TYR cc_start: 0.8237 (m-10) cc_final: 0.8013 (m-80) REVERT: B 832 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7422 (tp40) REVERT: B 848 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 880 LYS cc_start: 0.8295 (ptpp) cc_final: 0.7792 (ptpp) REVERT: B 885 LEU cc_start: 0.8477 (tp) cc_final: 0.8088 (tp) REVERT: B 888 GLU cc_start: 0.7558 (pt0) cc_final: 0.7102 (pt0) REVERT: B 889 HIS cc_start: 0.7375 (m90) cc_final: 0.7146 (m90) REVERT: B 899 ARG cc_start: 0.7823 (tmm-80) cc_final: 0.6981 (tmm-80) REVERT: B 902 ILE cc_start: 0.8930 (tt) cc_final: 0.8311 (tp) REVERT: B 903 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7966 (ttm170) REVERT: B 921 LEU cc_start: 0.8799 (tt) cc_final: 0.8388 (mm) REVERT: B 942 MET cc_start: 0.7905 (tpp) cc_final: 0.7705 (tpp) outliers start: 48 outliers final: 23 residues processed: 485 average time/residue: 0.2783 time to fit residues: 180.3233 Evaluate side-chains 480 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 449 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 613 GLN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10880 Z= 0.196 Angle : 0.618 10.481 14762 Z= 0.324 Chirality : 0.040 0.176 1782 Planarity : 0.004 0.040 1816 Dihedral : 6.304 58.773 1476 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.17 % Allowed : 20.86 % Favored : 73.97 % 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: 1.59 (0.23), residues: 1354 helix: 1.43 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.80 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 635 HIS 0.003 0.001 HIS A 600 PHE 0.017 0.001 PHE A 457 TYR 0.017 0.001 TYR B 837 ARG 0.004 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 462 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7964 (mt) cc_final: 0.7734 (mm) REVERT: A 113 LEU cc_start: 0.8196 (tt) cc_final: 0.7954 (tp) REVERT: A 134 ASP cc_start: 0.7862 (t70) cc_final: 0.7546 (t0) REVERT: A 155 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6079 (p0) REVERT: A 158 THR cc_start: 0.8186 (m) cc_final: 0.7447 (p) REVERT: A 161 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7152 (mmt180) REVERT: A 195 PHE cc_start: 0.7916 (t80) cc_final: 0.7674 (t80) REVERT: A 204 ILE cc_start: 0.8689 (mt) cc_final: 0.8365 (tt) REVERT: A 206 SER cc_start: 0.8244 (t) cc_final: 0.7755 (p) REVERT: A 238 ASP cc_start: 0.7343 (m-30) cc_final: 0.6815 (m-30) REVERT: A 248 PHE cc_start: 0.8068 (m-80) cc_final: 0.7420 (m-10) REVERT: A 251 MET cc_start: 0.7675 (ttm) cc_final: 0.7283 (ttm) REVERT: A 252 VAL cc_start: 0.7194 (t) cc_final: 0.6488 (m) REVERT: A 278 TRP cc_start: 0.8385 (t-100) cc_final: 0.7598 (t-100) REVERT: A 294 PHE cc_start: 0.7789 (m-80) cc_final: 0.7570 (m-80) REVERT: A 312 TYR cc_start: 0.8264 (t80) cc_final: 0.7803 (t80) REVERT: A 316 ASP cc_start: 0.7466 (m-30) cc_final: 0.7063 (m-30) REVERT: A 345 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7948 (m) REVERT: A 351 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7980 (tpp80) REVERT: A 364 ILE cc_start: 0.8066 (mt) cc_final: 0.7558 (tt) REVERT: A 384 ASP cc_start: 0.8123 (t0) cc_final: 0.7856 (t0) REVERT: A 393 LEU cc_start: 0.8859 (mp) cc_final: 0.8409 (mp) REVERT: A 396 THR cc_start: 0.8331 (m) cc_final: 0.8071 (p) REVERT: A 399 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7831 (tpt170) REVERT: A 401 MET cc_start: 0.7732 (ttm) cc_final: 0.7518 (ttm) REVERT: A 425 MET cc_start: 0.7960 (tpt) cc_final: 0.7269 (tpp) REVERT: A 443 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 449 ASP cc_start: 0.8489 (t0) cc_final: 0.8265 (t0) REVERT: A 466 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7872 (t) REVERT: A 480 ILE cc_start: 0.8413 (mt) cc_final: 0.8098 (mm) REVERT: A 485 ASP cc_start: 0.8102 (t0) cc_final: 0.7648 (t0) REVERT: A 486 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7483 (tp) REVERT: A 494 MET cc_start: 0.8125 (tpp) cc_final: 0.7690 (tpp) REVERT: A 499 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7857 (ttp80) REVERT: A 500 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7917 (ttt180) REVERT: A 501 ILE cc_start: 0.8671 (tt) cc_final: 0.8419 (pt) REVERT: A 502 HIS cc_start: 0.8201 (t70) cc_final: 0.7654 (t70) REVERT: A 505 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 506 ASN cc_start: 0.8483 (m-40) cc_final: 0.7831 (m110) REVERT: A 507 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7862 (ptp-110) REVERT: A 511 MET cc_start: 0.8230 (ttm) cc_final: 0.7560 (tmm) REVERT: A 523 TRP cc_start: 0.8018 (m100) cc_final: 0.7649 (m100) REVERT: A 585 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.8208 (tmm-80) REVERT: A 586 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7344 (ptm) REVERT: A 587 LEU cc_start: 0.8853 (pp) cc_final: 0.8281 (pp) REVERT: A 590 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 591 LYS cc_start: 0.8702 (pttp) cc_final: 0.8315 (pttp) REVERT: A 600 HIS cc_start: 0.7982 (t70) cc_final: 0.7552 (t70) REVERT: A 610 LEU cc_start: 0.8868 (tt) cc_final: 0.8095 (tp) REVERT: A 613 GLN cc_start: 0.8521 (pp30) cc_final: 0.7836 (pp30) REVERT: A 830 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 832 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 833 LEU cc_start: 0.8864 (tp) cc_final: 0.8651 (mm) REVERT: A 841 LYS cc_start: 0.8715 (mptt) cc_final: 0.8036 (tptt) REVERT: A 844 ILE cc_start: 0.9058 (mm) cc_final: 0.8534 (pt) REVERT: A 848 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 857 MET cc_start: 0.8001 (ppp) cc_final: 0.7196 (ppp) REVERT: A 875 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7212 (ttp80) REVERT: A 880 LYS cc_start: 0.8812 (pptt) cc_final: 0.8311 (pptt) REVERT: A 887 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7229 (mtm110) REVERT: A 888 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 899 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7394 (mtt90) REVERT: A 906 LEU cc_start: 0.8416 (mt) cc_final: 0.8055 (mm) REVERT: A 908 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7496 (t-90) REVERT: A 909 SER cc_start: 0.8681 (t) cc_final: 0.8435 (p) REVERT: A 911 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 923 ASP cc_start: 0.5466 (p0) cc_final: 0.5042 (p0) REVERT: A 926 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 938 MET cc_start: 0.8279 (tpp) cc_final: 0.8000 (tpp) REVERT: B 78 ILE cc_start: 0.8124 (tt) cc_final: 0.7635 (mt) REVERT: B 90 ILE cc_start: 0.8228 (mt) cc_final: 0.7946 (mm) REVERT: B 92 ARG cc_start: 0.8641 (mtp85) cc_final: 0.8341 (mmm-85) REVERT: B 109 LEU cc_start: 0.7816 (tp) cc_final: 0.7613 (tp) REVERT: B 112 ILE cc_start: 0.8180 (mt) cc_final: 0.7882 (mm) REVERT: B 154 MET cc_start: 0.7072 (ttm) cc_final: 0.6642 (mtm) REVERT: B 156 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8319 (t) REVERT: B 163 PHE cc_start: 0.8146 (t80) cc_final: 0.7627 (t80) REVERT: B 165 GLN cc_start: 0.8336 (pt0) cc_final: 0.7980 (pt0) REVERT: B 166 VAL cc_start: 0.8504 (t) cc_final: 0.8184 (p) REVERT: B 186 MET cc_start: 0.7801 (mmm) cc_final: 0.7465 (mmm) REVERT: B 189 PHE cc_start: 0.7943 (m-10) cc_final: 0.7276 (m-10) REVERT: B 191 TYR cc_start: 0.8513 (m-80) cc_final: 0.8000 (m-80) REVERT: B 197 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: B 199 MET cc_start: 0.7517 (tpt) cc_final: 0.7207 (tpp) REVERT: B 218 LYS cc_start: 0.8508 (ptmm) cc_final: 0.8174 (ptmm) REVERT: B 237 ASN cc_start: 0.7942 (t0) cc_final: 0.7561 (t0) REVERT: B 242 ILE cc_start: 0.8498 (mt) cc_final: 0.8197 (mm) REVERT: B 248 PHE cc_start: 0.8042 (m-80) cc_final: 0.7324 (m-80) REVERT: B 251 MET cc_start: 0.6870 (tmm) cc_final: 0.6475 (tmm) REVERT: B 263 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 293 ILE cc_start: 0.8424 (mt) cc_final: 0.8201 (tp) REVERT: B 321 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6784 (t) REVERT: B 335 ASN cc_start: 0.8238 (t0) cc_final: 0.7935 (t0) REVERT: B 338 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7287 (ptpt) REVERT: B 344 GLU cc_start: 0.7578 (pp20) cc_final: 0.7337 (pp20) REVERT: B 375 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7794 (ptpt) REVERT: B 383 MET cc_start: 0.7180 (tpp) cc_final: 0.5728 (tpp) REVERT: B 387 TYR cc_start: 0.7728 (m-10) cc_final: 0.7375 (m-80) REVERT: B 393 LEU cc_start: 0.8572 (mp) cc_final: 0.8339 (mp) REVERT: B 397 ILE cc_start: 0.8588 (mt) cc_final: 0.7678 (mm) REVERT: B 399 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8578 (ttt90) REVERT: B 401 MET cc_start: 0.7906 (mtp) cc_final: 0.7302 (mtp) REVERT: B 406 PHE cc_start: 0.8220 (m-80) cc_final: 0.7916 (m-80) REVERT: B 424 ILE cc_start: 0.8833 (tp) cc_final: 0.8624 (tp) REVERT: B 425 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7940 (mtp) REVERT: B 444 ASN cc_start: 0.8027 (t0) cc_final: 0.7768 (t0) REVERT: B 445 LEU cc_start: 0.8430 (tp) cc_final: 0.8128 (tp) REVERT: B 458 HIS cc_start: 0.8545 (m-70) cc_final: 0.8270 (m-70) REVERT: B 466 THR cc_start: 0.7686 (p) cc_final: 0.7427 (t) REVERT: B 470 ASN cc_start: 0.7695 (m-40) cc_final: 0.7433 (m110) REVERT: B 477 LEU cc_start: 0.8619 (mp) cc_final: 0.8227 (tp) REVERT: B 480 ILE cc_start: 0.8122 (mt) cc_final: 0.7864 (mt) REVERT: B 490 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8504 (ttmt) REVERT: B 491 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8259 (ttp-110) REVERT: B 494 MET cc_start: 0.7547 (tpp) cc_final: 0.7262 (tpp) REVERT: B 500 ARG cc_start: 0.7970 (tmt-80) cc_final: 0.7549 (ttt-90) REVERT: B 512 LEU cc_start: 0.8890 (mp) cc_final: 0.8485 (mm) REVERT: B 586 MET cc_start: 0.7746 (tpt) cc_final: 0.7401 (tpt) REVERT: B 590 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7129 (mt-10) REVERT: B 594 TYR cc_start: 0.8279 (m-10) cc_final: 0.8008 (m-80) REVERT: B 832 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7398 (tp40) REVERT: B 848 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 877 GLN cc_start: 0.8289 (pp30) cc_final: 0.7336 (pp30) REVERT: B 880 LYS cc_start: 0.8313 (ptpp) cc_final: 0.7796 (ptpp) REVERT: B 881 GLU cc_start: 0.7988 (pt0) cc_final: 0.7465 (pt0) REVERT: B 885 LEU cc_start: 0.8403 (tp) cc_final: 0.8055 (tp) REVERT: B 888 GLU cc_start: 0.7518 (pt0) cc_final: 0.7068 (pt0) REVERT: B 889 HIS cc_start: 0.7382 (m90) cc_final: 0.7147 (m90) REVERT: B 899 ARG cc_start: 0.7809 (tmm-80) cc_final: 0.7008 (tmm-80) REVERT: B 902 ILE cc_start: 0.8873 (tt) cc_final: 0.8274 (tp) REVERT: B 903 ARG cc_start: 0.8375 (ttm170) cc_final: 0.7993 (ttm170) REVERT: B 906 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 921 LEU cc_start: 0.8789 (tt) cc_final: 0.8416 (mm) REVERT: B 942 MET cc_start: 0.7915 (tpp) cc_final: 0.7677 (tpp) outliers start: 60 outliers final: 32 residues processed: 483 average time/residue: 0.2856 time to fit residues: 185.3748 Evaluate side-chains 501 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 455 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 165 GLN A 458 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 613 GLN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10880 Z= 0.211 Angle : 0.628 11.735 14762 Z= 0.329 Chirality : 0.041 0.242 1782 Planarity : 0.004 0.033 1816 Dihedral : 6.138 58.559 1471 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.03 % Allowed : 21.90 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1354 helix: 1.60 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.75 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 635 HIS 0.003 0.001 HIS A 914 PHE 0.018 0.001 PHE A 457 TYR 0.013 0.001 TYR B 837 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 458 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8219 (tt) cc_final: 0.7977 (tp) REVERT: A 134 ASP cc_start: 0.7890 (t70) cc_final: 0.7577 (t0) REVERT: A 154 MET cc_start: 0.7456 (tpp) cc_final: 0.6525 (mmt) REVERT: A 155 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.5931 (p0) REVERT: A 158 THR cc_start: 0.8156 (m) cc_final: 0.7395 (p) REVERT: A 161 ARG cc_start: 0.7593 (mmt180) cc_final: 0.7072 (mmt180) REVERT: A 204 ILE cc_start: 0.8708 (mt) cc_final: 0.8363 (tt) REVERT: A 205 MET cc_start: 0.7882 (mmp) cc_final: 0.7638 (mmm) REVERT: A 206 SER cc_start: 0.8243 (t) cc_final: 0.7741 (p) REVERT: A 231 GLU cc_start: 0.7781 (tt0) cc_final: 0.6809 (tt0) REVERT: A 233 GLU cc_start: 0.8346 (tt0) cc_final: 0.7920 (tt0) REVERT: A 238 ASP cc_start: 0.7244 (m-30) cc_final: 0.6707 (m-30) REVERT: A 248 PHE cc_start: 0.8083 (m-80) cc_final: 0.7349 (m-10) REVERT: A 251 MET cc_start: 0.7684 (ttm) cc_final: 0.7286 (ttm) REVERT: A 252 VAL cc_start: 0.7246 (t) cc_final: 0.6547 (m) REVERT: A 278 TRP cc_start: 0.8405 (t-100) cc_final: 0.7777 (t-100) REVERT: A 312 TYR cc_start: 0.8268 (t80) cc_final: 0.7827 (t80) REVERT: A 316 ASP cc_start: 0.7406 (m-30) cc_final: 0.6964 (m-30) REVERT: A 351 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7990 (tpp80) REVERT: A 364 ILE cc_start: 0.8027 (mt) cc_final: 0.7562 (tt) REVERT: A 384 ASP cc_start: 0.8152 (t0) cc_final: 0.7874 (t0) REVERT: A 393 LEU cc_start: 0.8831 (mp) cc_final: 0.8389 (mp) REVERT: A 396 THR cc_start: 0.8330 (m) cc_final: 0.8062 (p) REVERT: A 401 MET cc_start: 0.7693 (ttm) cc_final: 0.7479 (ttm) REVERT: A 420 ARG cc_start: 0.8196 (ptp90) cc_final: 0.7445 (mtm-85) REVERT: A 425 MET cc_start: 0.7997 (tpt) cc_final: 0.7122 (tpp) REVERT: A 427 TRP cc_start: 0.8512 (t-100) cc_final: 0.8307 (t-100) REVERT: A 443 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 466 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7904 (t) REVERT: A 480 ILE cc_start: 0.8447 (mt) cc_final: 0.8123 (mm) REVERT: A 485 ASP cc_start: 0.8100 (t0) cc_final: 0.7643 (t0) REVERT: A 486 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 494 MET cc_start: 0.8165 (tpp) cc_final: 0.7616 (tpp) REVERT: A 499 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7852 (ttp80) REVERT: A 500 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7908 (ttt180) REVERT: A 501 ILE cc_start: 0.8660 (tt) cc_final: 0.8410 (pt) REVERT: A 502 HIS cc_start: 0.8195 (t70) cc_final: 0.7651 (t70) REVERT: A 505 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 506 ASN cc_start: 0.8458 (m-40) cc_final: 0.7769 (m110) REVERT: A 507 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7870 (ptp-110) REVERT: A 511 MET cc_start: 0.8213 (ttm) cc_final: 0.7562 (tmm) REVERT: A 523 TRP cc_start: 0.8025 (m100) cc_final: 0.7706 (m100) REVERT: A 585 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8240 (tmm-80) REVERT: A 586 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7370 (ptm) REVERT: A 587 LEU cc_start: 0.8859 (pp) cc_final: 0.8240 (pp) REVERT: A 590 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 591 LYS cc_start: 0.8693 (pttp) cc_final: 0.8300 (pttp) REVERT: A 600 HIS cc_start: 0.7941 (t70) cc_final: 0.7500 (t70) REVERT: A 610 LEU cc_start: 0.8875 (tt) cc_final: 0.8109 (tp) REVERT: A 613 GLN cc_start: 0.8528 (pp30) cc_final: 0.7812 (pp30) REVERT: A 830 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7799 (t0) REVERT: A 832 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 841 LYS cc_start: 0.8741 (mptt) cc_final: 0.8201 (tptt) REVERT: A 848 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 857 MET cc_start: 0.7991 (ppp) cc_final: 0.7320 (ppp) REVERT: A 875 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7231 (ttp80) REVERT: A 880 LYS cc_start: 0.8840 (pptt) cc_final: 0.8325 (pptt) REVERT: A 887 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7462 (mtm110) REVERT: A 888 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 897 LYS cc_start: 0.8629 (pttt) cc_final: 0.8333 (pttt) REVERT: A 899 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7437 (mtt90) REVERT: A 906 LEU cc_start: 0.8408 (mt) cc_final: 0.8020 (mm) REVERT: A 908 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7533 (t-90) REVERT: A 909 SER cc_start: 0.8714 (t) cc_final: 0.8468 (p) REVERT: A 911 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 923 ASP cc_start: 0.5397 (p0) cc_final: 0.4991 (p0) REVERT: A 925 MET cc_start: 0.8497 (pmm) cc_final: 0.8163 (ppp) REVERT: A 938 MET cc_start: 0.8315 (tpp) cc_final: 0.8006 (tpp) REVERT: B 90 ILE cc_start: 0.8199 (mt) cc_final: 0.7914 (mm) REVERT: B 92 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8390 (mtp85) REVERT: B 109 LEU cc_start: 0.7815 (tp) cc_final: 0.7598 (tp) REVERT: B 112 ILE cc_start: 0.8191 (mt) cc_final: 0.7893 (mm) REVERT: B 154 MET cc_start: 0.7136 (ttm) cc_final: 0.6921 (ttm) REVERT: B 156 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 163 PHE cc_start: 0.8161 (t80) cc_final: 0.7576 (t80) REVERT: B 166 VAL cc_start: 0.8482 (t) cc_final: 0.8171 (p) REVERT: B 186 MET cc_start: 0.7897 (mmm) cc_final: 0.7522 (mmm) REVERT: B 189 PHE cc_start: 0.7941 (m-10) cc_final: 0.7356 (m-10) REVERT: B 191 TYR cc_start: 0.8527 (m-80) cc_final: 0.8124 (m-80) REVERT: B 199 MET cc_start: 0.7497 (tpt) cc_final: 0.6880 (tpp) REVERT: B 218 LYS cc_start: 0.8510 (ptmm) cc_final: 0.8176 (ptmm) REVERT: B 237 ASN cc_start: 0.7959 (t0) cc_final: 0.7547 (t0) REVERT: B 242 ILE cc_start: 0.8509 (mt) cc_final: 0.8224 (mm) REVERT: B 251 MET cc_start: 0.6750 (tmm) cc_final: 0.6416 (tmm) REVERT: B 263 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 293 ILE cc_start: 0.8506 (mt) cc_final: 0.8250 (tp) REVERT: B 321 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6847 (t) REVERT: B 335 ASN cc_start: 0.8254 (t0) cc_final: 0.6939 (t0) REVERT: B 338 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6766 (ptpt) REVERT: B 344 GLU cc_start: 0.7579 (pp20) cc_final: 0.7324 (pp20) REVERT: B 375 LYS cc_start: 0.8160 (ptpt) cc_final: 0.7811 (ptpt) REVERT: B 377 LEU cc_start: 0.7686 (tp) cc_final: 0.7234 (tp) REVERT: B 383 MET cc_start: 0.7168 (tpp) cc_final: 0.5681 (tpp) REVERT: B 387 TYR cc_start: 0.7732 (m-10) cc_final: 0.7396 (m-80) REVERT: B 393 LEU cc_start: 0.8605 (mp) cc_final: 0.8366 (mp) REVERT: B 397 ILE cc_start: 0.8600 (mt) cc_final: 0.7684 (mm) REVERT: B 399 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8606 (ttt90) REVERT: B 401 MET cc_start: 0.7970 (mtp) cc_final: 0.7329 (mtp) REVERT: B 406 PHE cc_start: 0.8255 (m-80) cc_final: 0.7979 (m-80) REVERT: B 413 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6319 (pt) REVERT: B 424 ILE cc_start: 0.8828 (tp) cc_final: 0.8616 (tp) REVERT: B 444 ASN cc_start: 0.8028 (t0) cc_final: 0.7774 (t0) REVERT: B 445 LEU cc_start: 0.8422 (tp) cc_final: 0.8138 (tp) REVERT: B 458 HIS cc_start: 0.8533 (m-70) cc_final: 0.8281 (m-70) REVERT: B 466 THR cc_start: 0.7678 (p) cc_final: 0.7423 (t) REVERT: B 470 ASN cc_start: 0.7683 (m-40) cc_final: 0.7426 (m110) REVERT: B 477 LEU cc_start: 0.8629 (mp) cc_final: 0.8233 (tp) REVERT: B 480 ILE cc_start: 0.8141 (mt) cc_final: 0.7879 (mt) REVERT: B 490 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8514 (ttmt) REVERT: B 491 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8255 (ttp-110) REVERT: B 494 MET cc_start: 0.7542 (tpp) cc_final: 0.7283 (tpp) REVERT: B 500 ARG cc_start: 0.7987 (tmt-80) cc_final: 0.7563 (ttt-90) REVERT: B 506 ASN cc_start: 0.8485 (m-40) cc_final: 0.8270 (m-40) REVERT: B 512 LEU cc_start: 0.8892 (mp) cc_final: 0.8465 (mm) REVERT: B 517 PHE cc_start: 0.7205 (m-10) cc_final: 0.6636 (m-10) REVERT: B 579 MET cc_start: 0.6108 (mmm) cc_final: 0.5859 (mmm) REVERT: B 583 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7223 (ttp-110) REVERT: B 586 MET cc_start: 0.7741 (tpt) cc_final: 0.7389 (tpt) REVERT: B 590 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 594 TYR cc_start: 0.8256 (m-10) cc_final: 0.8015 (m-80) REVERT: B 826 ASN cc_start: 0.8222 (m110) cc_final: 0.7956 (m-40) REVERT: B 832 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7453 (tp40) REVERT: B 848 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 863 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5730 (pt) REVERT: B 877 GLN cc_start: 0.8298 (pp30) cc_final: 0.7356 (pp30) REVERT: B 880 LYS cc_start: 0.8322 (ptpp) cc_final: 0.7803 (ptpp) REVERT: B 881 GLU cc_start: 0.8022 (pt0) cc_final: 0.7493 (pt0) REVERT: B 885 LEU cc_start: 0.8410 (tp) cc_final: 0.7993 (tp) REVERT: B 888 GLU cc_start: 0.7536 (pt0) cc_final: 0.7085 (pt0) REVERT: B 899 ARG cc_start: 0.7861 (tmm-80) cc_final: 0.7071 (tmm-80) REVERT: B 902 ILE cc_start: 0.8854 (tt) cc_final: 0.8177 (tp) REVERT: B 903 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8025 (ttm170) REVERT: B 904 THR cc_start: 0.8201 (m) cc_final: 0.7955 (p) REVERT: B 906 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8390 (mm) REVERT: B 921 LEU cc_start: 0.8805 (tt) cc_final: 0.8450 (mm) REVERT: B 931 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 942 MET cc_start: 0.7919 (tpp) cc_final: 0.7684 (tpp) outliers start: 70 outliers final: 39 residues processed: 485 average time/residue: 0.2670 time to fit residues: 173.3050 Evaluate side-chains 507 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 454 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 270 GLN A 458 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN B 421 ASN B 613 GLN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.199 Angle : 0.635 13.335 14762 Z= 0.329 Chirality : 0.041 0.194 1782 Planarity : 0.004 0.035 1816 Dihedral : 6.089 57.631 1471 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.52 % Allowed : 23.53 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1354 helix: 1.69 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.88 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 635 HIS 0.002 0.000 HIS B 614 PHE 0.017 0.001 PHE A 457 TYR 0.016 0.001 TYR B 837 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 454 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8242 (tt) cc_final: 0.7994 (tp) REVERT: A 134 ASP cc_start: 0.7917 (t70) cc_final: 0.7563 (t0) REVERT: A 154 MET cc_start: 0.7391 (tpp) cc_final: 0.7143 (tpp) REVERT: A 155 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6040 (p0) REVERT: A 158 THR cc_start: 0.8131 (m) cc_final: 0.7377 (p) REVERT: A 161 ARG cc_start: 0.7508 (mmt180) cc_final: 0.7086 (mmt180) REVERT: A 204 ILE cc_start: 0.8707 (mt) cc_final: 0.8356 (tt) REVERT: A 206 SER cc_start: 0.8246 (t) cc_final: 0.7710 (p) REVERT: A 233 GLU cc_start: 0.8366 (tt0) cc_final: 0.8056 (tt0) REVERT: A 238 ASP cc_start: 0.7189 (m-30) cc_final: 0.6676 (m-30) REVERT: A 248 PHE cc_start: 0.8075 (m-80) cc_final: 0.7523 (m-10) REVERT: A 252 VAL cc_start: 0.7185 (t) cc_final: 0.6536 (m) REVERT: A 278 TRP cc_start: 0.8397 (t-100) cc_final: 0.7837 (t-100) REVERT: A 312 TYR cc_start: 0.8270 (t80) cc_final: 0.7725 (t80) REVERT: A 316 ASP cc_start: 0.7417 (m-30) cc_final: 0.7131 (m-30) REVERT: A 345 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7980 (m) REVERT: A 351 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7968 (tpp80) REVERT: A 364 ILE cc_start: 0.8011 (mt) cc_final: 0.7569 (tt) REVERT: A 384 ASP cc_start: 0.8143 (t0) cc_final: 0.7871 (t0) REVERT: A 393 LEU cc_start: 0.8817 (mp) cc_final: 0.8327 (mp) REVERT: A 396 THR cc_start: 0.8326 (m) cc_final: 0.8058 (p) REVERT: A 401 MET cc_start: 0.7686 (ttm) cc_final: 0.7484 (ttm) REVERT: A 420 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7624 (mtm-85) REVERT: A 425 MET cc_start: 0.8108 (tpt) cc_final: 0.7311 (tpp) REVERT: A 443 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 449 ASP cc_start: 0.8359 (t0) cc_final: 0.8121 (t0) REVERT: A 466 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7919 (t) REVERT: A 475 GLN cc_start: 0.8580 (tp40) cc_final: 0.8290 (mm-40) REVERT: A 480 ILE cc_start: 0.8439 (mt) cc_final: 0.8086 (mm) REVERT: A 485 ASP cc_start: 0.8101 (t0) cc_final: 0.7690 (t0) REVERT: A 486 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7460 (tp) REVERT: A 494 MET cc_start: 0.8104 (tpp) cc_final: 0.7532 (tpp) REVERT: A 499 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7865 (ttp80) REVERT: A 500 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7902 (ttt180) REVERT: A 502 HIS cc_start: 0.8199 (t70) cc_final: 0.7680 (t70) REVERT: A 505 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 506 ASN cc_start: 0.8474 (m-40) cc_final: 0.7745 (m110) REVERT: A 507 ARG cc_start: 0.8165 (ptp-110) cc_final: 0.7855 (ptp-110) REVERT: A 511 MET cc_start: 0.8214 (ttm) cc_final: 0.7575 (tmm) REVERT: A 523 TRP cc_start: 0.7995 (m100) cc_final: 0.7672 (m100) REVERT: A 586 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7405 (ptm) REVERT: A 587 LEU cc_start: 0.8863 (pp) cc_final: 0.8252 (pp) REVERT: A 590 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8148 (mt-10) REVERT: A 591 LYS cc_start: 0.8680 (pttp) cc_final: 0.8289 (pttp) REVERT: A 600 HIS cc_start: 0.7866 (t70) cc_final: 0.7461 (t70) REVERT: A 610 LEU cc_start: 0.8876 (tt) cc_final: 0.8118 (tp) REVERT: A 613 GLN cc_start: 0.8528 (pp30) cc_final: 0.8036 (pp30) REVERT: A 830 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 832 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 841 LYS cc_start: 0.8738 (mptt) cc_final: 0.8204 (tptt) REVERT: A 844 ILE cc_start: 0.9074 (mm) cc_final: 0.8527 (mm) REVERT: A 848 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 857 MET cc_start: 0.8016 (ppp) cc_final: 0.7556 (ppp) REVERT: A 875 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7308 (ttp80) REVERT: A 888 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 897 LYS cc_start: 0.8620 (pttt) cc_final: 0.8243 (pttt) REVERT: A 899 ARG cc_start: 0.7747 (mtt90) cc_final: 0.7394 (mtt90) REVERT: A 906 LEU cc_start: 0.8389 (mt) cc_final: 0.8011 (mm) REVERT: A 908 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7489 (t-90) REVERT: A 909 SER cc_start: 0.8714 (t) cc_final: 0.8470 (p) REVERT: A 911 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6953 (mt-10) REVERT: A 923 ASP cc_start: 0.5504 (p0) cc_final: 0.5147 (p0) REVERT: A 925 MET cc_start: 0.8484 (pmm) cc_final: 0.8164 (ppp) REVERT: A 938 MET cc_start: 0.8325 (tpp) cc_final: 0.7999 (tpp) REVERT: B 92 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8435 (mtp85) REVERT: B 109 LEU cc_start: 0.7818 (tp) cc_final: 0.7576 (tp) REVERT: B 112 ILE cc_start: 0.8196 (mt) cc_final: 0.7903 (mm) REVERT: B 156 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8319 (t) REVERT: B 163 PHE cc_start: 0.8180 (t80) cc_final: 0.7618 (t80) REVERT: B 166 VAL cc_start: 0.8535 (t) cc_final: 0.8205 (p) REVERT: B 186 MET cc_start: 0.7895 (mmm) cc_final: 0.7500 (mmm) REVERT: B 189 PHE cc_start: 0.7960 (m-10) cc_final: 0.7451 (m-10) REVERT: B 191 TYR cc_start: 0.8504 (m-80) cc_final: 0.8181 (m-80) REVERT: B 199 MET cc_start: 0.7503 (tpt) cc_final: 0.6833 (tpp) REVERT: B 205 MET cc_start: 0.8047 (tpp) cc_final: 0.7799 (mmp) REVERT: B 218 LYS cc_start: 0.8516 (ptmm) cc_final: 0.8168 (ptmm) REVERT: B 237 ASN cc_start: 0.7940 (t0) cc_final: 0.7545 (t0) REVERT: B 242 ILE cc_start: 0.8526 (mt) cc_final: 0.8234 (mm) REVERT: B 251 MET cc_start: 0.6728 (tmm) cc_final: 0.6385 (tmm) REVERT: B 263 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 293 ILE cc_start: 0.8505 (mt) cc_final: 0.8247 (tp) REVERT: B 335 ASN cc_start: 0.8262 (t0) cc_final: 0.6933 (t0) REVERT: B 338 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6641 (ptpt) REVERT: B 344 GLU cc_start: 0.7584 (pp20) cc_final: 0.7328 (pp20) REVERT: B 375 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7811 (ptpt) REVERT: B 377 LEU cc_start: 0.7700 (tp) cc_final: 0.7230 (tp) REVERT: B 383 MET cc_start: 0.7147 (tpp) cc_final: 0.6043 (tpp) REVERT: B 387 TYR cc_start: 0.7715 (m-10) cc_final: 0.7392 (m-80) REVERT: B 393 LEU cc_start: 0.8609 (mp) cc_final: 0.8378 (mp) REVERT: B 397 ILE cc_start: 0.8660 (mt) cc_final: 0.7720 (mm) REVERT: B 399 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8582 (ttt90) REVERT: B 401 MET cc_start: 0.7951 (mtp) cc_final: 0.7324 (mtp) REVERT: B 406 PHE cc_start: 0.8273 (m-80) cc_final: 0.8009 (m-80) REVERT: B 413 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.4819 (mp) REVERT: B 424 ILE cc_start: 0.8837 (tp) cc_final: 0.8592 (tp) REVERT: B 444 ASN cc_start: 0.8008 (t0) cc_final: 0.7786 (t0) REVERT: B 445 LEU cc_start: 0.8455 (tp) cc_final: 0.8220 (tp) REVERT: B 458 HIS cc_start: 0.8530 (m-70) cc_final: 0.8262 (m-70) REVERT: B 466 THR cc_start: 0.7632 (p) cc_final: 0.7373 (t) REVERT: B 470 ASN cc_start: 0.7657 (m-40) cc_final: 0.7361 (m110) REVERT: B 477 LEU cc_start: 0.8631 (mp) cc_final: 0.8238 (tp) REVERT: B 480 ILE cc_start: 0.8120 (mt) cc_final: 0.7870 (mt) REVERT: B 490 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8572 (ttmt) REVERT: B 491 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8253 (ttp-110) REVERT: B 494 MET cc_start: 0.7557 (tpp) cc_final: 0.7280 (tpp) REVERT: B 500 ARG cc_start: 0.8011 (tmt-80) cc_final: 0.7433 (ttt-90) REVERT: B 506 ASN cc_start: 0.8494 (m-40) cc_final: 0.8281 (m-40) REVERT: B 512 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 517 PHE cc_start: 0.7177 (m-10) cc_final: 0.6715 (m-10) REVERT: B 583 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7253 (ttp-110) REVERT: B 586 MET cc_start: 0.7699 (tpt) cc_final: 0.7309 (tpt) REVERT: B 590 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 832 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7265 (tp40) REVERT: B 848 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 877 GLN cc_start: 0.8289 (pp30) cc_final: 0.7741 (pp30) REVERT: B 880 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7800 (ptpp) REVERT: B 885 LEU cc_start: 0.8410 (tp) cc_final: 0.8151 (tp) REVERT: B 899 ARG cc_start: 0.7885 (tmm-80) cc_final: 0.7096 (tmm-80) REVERT: B 902 ILE cc_start: 0.8828 (tt) cc_final: 0.8102 (tp) REVERT: B 903 ARG cc_start: 0.8457 (ttm170) cc_final: 0.8034 (ttm170) REVERT: B 904 THR cc_start: 0.8240 (m) cc_final: 0.8006 (p) REVERT: B 906 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 921 LEU cc_start: 0.8826 (tt) cc_final: 0.8565 (mm) REVERT: B 931 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 942 MET cc_start: 0.7899 (tpp) cc_final: 0.7663 (tpp) outliers start: 64 outliers final: 39 residues processed: 474 average time/residue: 0.2748 time to fit residues: 173.8801 Evaluate side-chains 496 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 442 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN B 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.186 Angle : 0.646 12.543 14762 Z= 0.337 Chirality : 0.041 0.205 1782 Planarity : 0.004 0.036 1816 Dihedral : 6.020 59.127 1470 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.26 % Allowed : 24.66 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1354 helix: 1.70 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.87 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 643 HIS 0.002 0.000 HIS A 614 PHE 0.023 0.001 PHE B 457 TYR 0.026 0.001 TYR B 594 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 445 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8204 (tt) cc_final: 0.7962 (tp) REVERT: A 134 ASP cc_start: 0.7979 (t70) cc_final: 0.7653 (t0) REVERT: A 154 MET cc_start: 0.7306 (tpp) cc_final: 0.6122 (mmt) REVERT: A 155 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.5987 (p0) REVERT: A 158 THR cc_start: 0.8116 (m) cc_final: 0.7347 (p) REVERT: A 161 ARG cc_start: 0.7497 (mmt180) cc_final: 0.7096 (mmt180) REVERT: A 199 MET cc_start: 0.7900 (tpt) cc_final: 0.7652 (tpp) REVERT: A 204 ILE cc_start: 0.8691 (mt) cc_final: 0.8340 (tt) REVERT: A 206 SER cc_start: 0.8218 (t) cc_final: 0.7680 (p) REVERT: A 231 GLU cc_start: 0.7711 (tt0) cc_final: 0.6639 (tt0) REVERT: A 233 GLU cc_start: 0.8284 (tt0) cc_final: 0.7933 (tt0) REVERT: A 238 ASP cc_start: 0.7153 (m-30) cc_final: 0.6651 (m-30) REVERT: A 248 PHE cc_start: 0.8087 (m-80) cc_final: 0.7467 (m-10) REVERT: A 252 VAL cc_start: 0.7203 (t) cc_final: 0.6556 (m) REVERT: A 278 TRP cc_start: 0.8387 (t-100) cc_final: 0.7814 (t-100) REVERT: A 312 TYR cc_start: 0.8278 (t80) cc_final: 0.7738 (t80) REVERT: A 316 ASP cc_start: 0.7427 (m-30) cc_final: 0.6862 (m-30) REVERT: A 345 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7974 (m) REVERT: A 351 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7970 (tpp80) REVERT: A 364 ILE cc_start: 0.7922 (mt) cc_final: 0.7467 (tt) REVERT: A 384 ASP cc_start: 0.8134 (t0) cc_final: 0.7866 (t0) REVERT: A 393 LEU cc_start: 0.8800 (mp) cc_final: 0.8318 (mp) REVERT: A 396 THR cc_start: 0.8330 (m) cc_final: 0.8056 (p) REVERT: A 401 MET cc_start: 0.7686 (ttm) cc_final: 0.7439 (ttm) REVERT: A 420 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7529 (mtm-85) REVERT: A 425 MET cc_start: 0.8216 (tpt) cc_final: 0.7469 (tpp) REVERT: A 443 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 449 ASP cc_start: 0.8397 (t0) cc_final: 0.8147 (t0) REVERT: A 466 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (t) REVERT: A 475 GLN cc_start: 0.8579 (tp40) cc_final: 0.8282 (mm-40) REVERT: A 480 ILE cc_start: 0.8384 (mt) cc_final: 0.8027 (mm) REVERT: A 485 ASP cc_start: 0.8059 (t0) cc_final: 0.7680 (t0) REVERT: A 486 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7930 (mp) REVERT: A 494 MET cc_start: 0.8111 (tpp) cc_final: 0.7510 (tpp) REVERT: A 499 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7868 (ttp80) REVERT: A 500 ARG cc_start: 0.8277 (ttt90) cc_final: 0.7930 (ttt180) REVERT: A 501 ILE cc_start: 0.8699 (tt) cc_final: 0.8461 (pt) REVERT: A 502 HIS cc_start: 0.8182 (t70) cc_final: 0.7640 (t70) REVERT: A 505 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 506 ASN cc_start: 0.8487 (m-40) cc_final: 0.7805 (m110) REVERT: A 507 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7857 (ptp-110) REVERT: A 511 MET cc_start: 0.8220 (ttm) cc_final: 0.7612 (tmm) REVERT: A 523 TRP cc_start: 0.7966 (m100) cc_final: 0.7611 (m100) REVERT: A 585 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8151 (tmm-80) REVERT: A 586 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7382 (ptm) REVERT: A 587 LEU cc_start: 0.8854 (pp) cc_final: 0.8234 (pp) REVERT: A 590 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8106 (mt-10) REVERT: A 591 LYS cc_start: 0.8671 (pttp) cc_final: 0.8263 (pttp) REVERT: A 600 HIS cc_start: 0.7892 (t70) cc_final: 0.7475 (t70) REVERT: A 610 LEU cc_start: 0.8850 (tt) cc_final: 0.8078 (tp) REVERT: A 613 GLN cc_start: 0.8572 (pp30) cc_final: 0.7946 (pp30) REVERT: A 647 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8532 (mtmm) REVERT: A 830 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7746 (t0) REVERT: A 832 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 841 LYS cc_start: 0.8732 (mptt) cc_final: 0.8259 (tptt) REVERT: A 844 ILE cc_start: 0.9060 (mm) cc_final: 0.8550 (mm) REVERT: A 847 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7961 (mp0) REVERT: A 848 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 857 MET cc_start: 0.7903 (ppp) cc_final: 0.7443 (ppp) REVERT: A 866 GLU cc_start: 0.7723 (tm-30) cc_final: 0.6078 (tp30) REVERT: A 875 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7268 (ttp80) REVERT: A 888 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 897 LYS cc_start: 0.8614 (pttt) cc_final: 0.8245 (pttt) REVERT: A 899 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7434 (mtt90) REVERT: A 906 LEU cc_start: 0.8379 (mt) cc_final: 0.8000 (mm) REVERT: A 908 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7539 (t-90) REVERT: A 909 SER cc_start: 0.8712 (t) cc_final: 0.8488 (p) REVERT: A 911 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 938 MET cc_start: 0.8337 (tpp) cc_final: 0.7994 (tpp) REVERT: B 92 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8446 (mtp85) REVERT: B 109 LEU cc_start: 0.7810 (tp) cc_final: 0.7581 (tp) REVERT: B 112 ILE cc_start: 0.8168 (mt) cc_final: 0.7885 (mm) REVERT: B 156 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (t) REVERT: B 163 PHE cc_start: 0.8196 (t80) cc_final: 0.7612 (t80) REVERT: B 166 VAL cc_start: 0.8522 (t) cc_final: 0.8201 (p) REVERT: B 189 PHE cc_start: 0.7928 (m-10) cc_final: 0.7438 (m-10) REVERT: B 191 TYR cc_start: 0.8520 (m-80) cc_final: 0.8244 (m-80) REVERT: B 199 MET cc_start: 0.7486 (tpt) cc_final: 0.6826 (tpp) REVERT: B 205 MET cc_start: 0.8055 (tpp) cc_final: 0.7804 (mmp) REVERT: B 218 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8148 (ptmm) REVERT: B 233 GLU cc_start: 0.7980 (tt0) cc_final: 0.7583 (tt0) REVERT: B 237 ASN cc_start: 0.7919 (t0) cc_final: 0.7540 (t0) REVERT: B 242 ILE cc_start: 0.8495 (mt) cc_final: 0.8216 (mm) REVERT: B 248 PHE cc_start: 0.8030 (m-80) cc_final: 0.7482 (m-80) REVERT: B 251 MET cc_start: 0.6719 (tmm) cc_final: 0.6373 (tmm) REVERT: B 263 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 293 ILE cc_start: 0.8484 (mt) cc_final: 0.8216 (tp) REVERT: B 335 ASN cc_start: 0.8258 (t0) cc_final: 0.6977 (t0) REVERT: B 337 GLU cc_start: 0.7296 (tp30) cc_final: 0.6397 (mp0) REVERT: B 338 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6536 (ptpt) REVERT: B 344 GLU cc_start: 0.7576 (pp20) cc_final: 0.7325 (pp20) REVERT: B 375 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7803 (ptpt) REVERT: B 377 LEU cc_start: 0.7732 (tp) cc_final: 0.7260 (tp) REVERT: B 383 MET cc_start: 0.7256 (tpp) cc_final: 0.5914 (tpp) REVERT: B 386 PHE cc_start: 0.7716 (t80) cc_final: 0.7321 (t80) REVERT: B 387 TYR cc_start: 0.7700 (m-10) cc_final: 0.7295 (m-80) REVERT: B 393 LEU cc_start: 0.8602 (mp) cc_final: 0.8373 (mp) REVERT: B 397 ILE cc_start: 0.8610 (mt) cc_final: 0.7676 (mm) REVERT: B 401 MET cc_start: 0.7917 (mtp) cc_final: 0.7292 (mtp) REVERT: B 406 PHE cc_start: 0.8257 (m-80) cc_final: 0.8021 (m-80) REVERT: B 413 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.4819 (mp) REVERT: B 424 ILE cc_start: 0.8828 (tp) cc_final: 0.8597 (tp) REVERT: B 444 ASN cc_start: 0.8014 (t0) cc_final: 0.7788 (t0) REVERT: B 445 LEU cc_start: 0.8447 (tp) cc_final: 0.8199 (tp) REVERT: B 466 THR cc_start: 0.7616 (p) cc_final: 0.7353 (t) REVERT: B 470 ASN cc_start: 0.7714 (m-40) cc_final: 0.7427 (m110) REVERT: B 477 LEU cc_start: 0.8612 (mp) cc_final: 0.8229 (tp) REVERT: B 480 ILE cc_start: 0.8108 (mt) cc_final: 0.7860 (mt) REVERT: B 490 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8583 (ttmt) REVERT: B 494 MET cc_start: 0.7557 (tpp) cc_final: 0.7269 (tpp) REVERT: B 500 ARG cc_start: 0.7964 (tmt-80) cc_final: 0.7400 (ttt-90) REVERT: B 505 GLN cc_start: 0.8505 (mt0) cc_final: 0.8301 (mt0) REVERT: B 506 ASN cc_start: 0.8473 (m-40) cc_final: 0.8263 (m-40) REVERT: B 512 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 517 PHE cc_start: 0.7177 (m-10) cc_final: 0.6650 (m-10) REVERT: B 580 GLU cc_start: 0.7091 (tp30) cc_final: 0.6234 (tp30) REVERT: B 583 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7170 (ttp-110) REVERT: B 586 MET cc_start: 0.7712 (tpt) cc_final: 0.7407 (tpt) REVERT: B 590 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 823 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8773 (mm) REVERT: B 832 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7268 (tm-30) REVERT: B 833 LEU cc_start: 0.8776 (tt) cc_final: 0.8301 (pp) REVERT: B 848 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 877 GLN cc_start: 0.8307 (pp30) cc_final: 0.7361 (pp30) REVERT: B 880 LYS cc_start: 0.8312 (ptpp) cc_final: 0.7807 (ptpp) REVERT: B 881 GLU cc_start: 0.7970 (pt0) cc_final: 0.7460 (pt0) REVERT: B 899 ARG cc_start: 0.7899 (tmm-80) cc_final: 0.7109 (tmm-80) REVERT: B 902 ILE cc_start: 0.8819 (tt) cc_final: 0.8075 (tp) REVERT: B 903 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8102 (ttm170) REVERT: B 904 THR cc_start: 0.8234 (m) cc_final: 0.8011 (p) REVERT: B 906 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 921 LEU cc_start: 0.8810 (tt) cc_final: 0.8541 (mm) REVERT: B 931 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 942 MET cc_start: 0.7889 (tpp) cc_final: 0.7666 (tpp) outliers start: 61 outliers final: 37 residues processed: 464 average time/residue: 0.2811 time to fit residues: 173.7824 Evaluate side-chains 497 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 445 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10880 Z= 0.199 Angle : 0.663 12.965 14762 Z= 0.341 Chirality : 0.042 0.208 1782 Planarity : 0.004 0.033 1816 Dihedral : 5.840 59.325 1468 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.09 % Allowed : 25.60 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1354 helix: 1.72 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.73 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 635 HIS 0.002 0.000 HIS A 458 PHE 0.040 0.001 PHE B 575 TYR 0.024 0.001 TYR B 837 ARG 0.005 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 457 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8300 (tptm) cc_final: 0.8080 (tptm) REVERT: A 113 LEU cc_start: 0.8220 (tt) cc_final: 0.7983 (tp) REVERT: A 134 ASP cc_start: 0.7994 (t70) cc_final: 0.7679 (t0) REVERT: A 154 MET cc_start: 0.7272 (tpp) cc_final: 0.7002 (tpp) REVERT: A 155 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.5950 (p0) REVERT: A 158 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7456 (p) REVERT: A 161 ARG cc_start: 0.7539 (mmt180) cc_final: 0.6980 (mmt-90) REVERT: A 199 MET cc_start: 0.7910 (tpt) cc_final: 0.7655 (tpp) REVERT: A 204 ILE cc_start: 0.8695 (mt) cc_final: 0.8336 (tt) REVERT: A 206 SER cc_start: 0.8222 (t) cc_final: 0.7447 (p) REVERT: A 233 GLU cc_start: 0.8294 (tt0) cc_final: 0.7950 (tt0) REVERT: A 237 ASN cc_start: 0.8131 (t0) cc_final: 0.7575 (t0) REVERT: A 238 ASP cc_start: 0.7157 (m-30) cc_final: 0.6655 (m-30) REVERT: A 248 PHE cc_start: 0.8059 (m-80) cc_final: 0.7479 (m-10) REVERT: A 252 VAL cc_start: 0.7197 (t) cc_final: 0.6560 (m) REVERT: A 278 TRP cc_start: 0.8383 (t-100) cc_final: 0.7852 (t-100) REVERT: A 312 TYR cc_start: 0.8268 (t80) cc_final: 0.7717 (t80) REVERT: A 316 ASP cc_start: 0.7399 (m-30) cc_final: 0.6807 (m-30) REVERT: A 345 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7973 (m) REVERT: A 351 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7976 (tpp80) REVERT: A 364 ILE cc_start: 0.7997 (mt) cc_final: 0.7587 (tt) REVERT: A 384 ASP cc_start: 0.8138 (t0) cc_final: 0.7872 (t0) REVERT: A 393 LEU cc_start: 0.8800 (mp) cc_final: 0.8307 (mp) REVERT: A 396 THR cc_start: 0.8309 (m) cc_final: 0.8040 (p) REVERT: A 401 MET cc_start: 0.7697 (ttm) cc_final: 0.7451 (ttm) REVERT: A 420 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7498 (mtm-85) REVERT: A 425 MET cc_start: 0.8234 (tpt) cc_final: 0.7576 (tpp) REVERT: A 443 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 444 ASN cc_start: 0.8299 (t0) cc_final: 0.8018 (t0) REVERT: A 449 ASP cc_start: 0.8429 (t0) cc_final: 0.8213 (t0) REVERT: A 466 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 475 GLN cc_start: 0.8584 (tp40) cc_final: 0.8272 (mm-40) REVERT: A 485 ASP cc_start: 0.8048 (t0) cc_final: 0.7699 (t0) REVERT: A 486 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 491 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8041 (ptp90) REVERT: A 494 MET cc_start: 0.8104 (tpp) cc_final: 0.7481 (tpp) REVERT: A 499 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7878 (ttp80) REVERT: A 500 ARG cc_start: 0.8273 (ttt90) cc_final: 0.7925 (ttt180) REVERT: A 501 ILE cc_start: 0.8716 (tt) cc_final: 0.8469 (pt) REVERT: A 505 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 506 ASN cc_start: 0.8498 (m-40) cc_final: 0.8031 (m-40) REVERT: A 507 ARG cc_start: 0.8194 (ptp-110) cc_final: 0.7877 (ptp-110) REVERT: A 511 MET cc_start: 0.8229 (ttm) cc_final: 0.7630 (tmm) REVERT: A 517 PHE cc_start: 0.8279 (m-10) cc_final: 0.7995 (m-80) REVERT: A 523 TRP cc_start: 0.7995 (m100) cc_final: 0.7626 (m100) REVERT: A 532 ILE cc_start: 0.8063 (mm) cc_final: 0.7734 (mm) REVERT: A 585 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8247 (tmm-80) REVERT: A 586 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7468 (ptm) REVERT: A 587 LEU cc_start: 0.8866 (pp) cc_final: 0.8266 (pp) REVERT: A 590 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 591 LYS cc_start: 0.8666 (pttp) cc_final: 0.8318 (pttp) REVERT: A 600 HIS cc_start: 0.7886 (t70) cc_final: 0.7459 (t70) REVERT: A 610 LEU cc_start: 0.8848 (tt) cc_final: 0.8087 (tp) REVERT: A 613 GLN cc_start: 0.8566 (pp30) cc_final: 0.7983 (pp30) REVERT: A 832 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 841 LYS cc_start: 0.8742 (mptt) cc_final: 0.8256 (tptt) REVERT: A 844 ILE cc_start: 0.9061 (mm) cc_final: 0.8513 (mt) REVERT: A 848 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 857 MET cc_start: 0.7957 (ppp) cc_final: 0.7564 (ppp) REVERT: A 875 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7358 (ttp80) REVERT: A 888 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 897 LYS cc_start: 0.8659 (pttt) cc_final: 0.8280 (pttt) REVERT: A 899 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7378 (mtt90) REVERT: A 906 LEU cc_start: 0.8378 (mt) cc_final: 0.8008 (mm) REVERT: A 908 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7515 (t-90) REVERT: A 909 SER cc_start: 0.8710 (t) cc_final: 0.8479 (p) REVERT: A 911 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 926 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 938 MET cc_start: 0.8332 (tpp) cc_final: 0.7983 (tpp) REVERT: B 92 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8461 (mtp85) REVERT: B 109 LEU cc_start: 0.7870 (tp) cc_final: 0.7648 (tp) REVERT: B 112 ILE cc_start: 0.8179 (mt) cc_final: 0.7893 (mm) REVERT: B 154 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6895 (mtm) REVERT: B 156 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 163 PHE cc_start: 0.8196 (t80) cc_final: 0.7636 (t80) REVERT: B 166 VAL cc_start: 0.8533 (t) cc_final: 0.8213 (p) REVERT: B 189 PHE cc_start: 0.7888 (m-10) cc_final: 0.7448 (m-10) REVERT: B 191 TYR cc_start: 0.8541 (m-80) cc_final: 0.8258 (m-80) REVERT: B 199 MET cc_start: 0.7516 (tpt) cc_final: 0.6882 (tpp) REVERT: B 205 MET cc_start: 0.8060 (tpp) cc_final: 0.7805 (mmp) REVERT: B 218 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8153 (ptmm) REVERT: B 237 ASN cc_start: 0.7933 (t0) cc_final: 0.7696 (t0) REVERT: B 242 ILE cc_start: 0.8503 (mt) cc_final: 0.8229 (mm) REVERT: B 248 PHE cc_start: 0.8043 (m-80) cc_final: 0.7491 (m-80) REVERT: B 251 MET cc_start: 0.6818 (tmm) cc_final: 0.6536 (tmm) REVERT: B 263 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 293 ILE cc_start: 0.8444 (mt) cc_final: 0.8228 (tp) REVERT: B 335 ASN cc_start: 0.8271 (t0) cc_final: 0.7917 (t0) REVERT: B 337 GLU cc_start: 0.7317 (tp30) cc_final: 0.6885 (mp0) REVERT: B 338 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7023 (ptpt) REVERT: B 344 GLU cc_start: 0.7585 (pp20) cc_final: 0.7333 (pp20) REVERT: B 366 MET cc_start: 0.7613 (ttm) cc_final: 0.7407 (mtm) REVERT: B 375 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7809 (ptpt) REVERT: B 377 LEU cc_start: 0.7707 (tp) cc_final: 0.7216 (tp) REVERT: B 383 MET cc_start: 0.7277 (tpp) cc_final: 0.5944 (tpp) REVERT: B 386 PHE cc_start: 0.7728 (t80) cc_final: 0.7335 (t80) REVERT: B 387 TYR cc_start: 0.7737 (m-10) cc_final: 0.7330 (m-80) REVERT: B 393 LEU cc_start: 0.8626 (mp) cc_final: 0.8294 (mp) REVERT: B 396 THR cc_start: 0.8422 (m) cc_final: 0.7972 (p) REVERT: B 397 ILE cc_start: 0.8566 (mt) cc_final: 0.8271 (mm) REVERT: B 406 PHE cc_start: 0.8299 (m-80) cc_final: 0.8050 (m-80) REVERT: B 413 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.4948 (mp) REVERT: B 424 ILE cc_start: 0.8848 (tp) cc_final: 0.8601 (tp) REVERT: B 444 ASN cc_start: 0.8006 (t0) cc_final: 0.7788 (t0) REVERT: B 445 LEU cc_start: 0.8452 (tp) cc_final: 0.8197 (tp) REVERT: B 466 THR cc_start: 0.7622 (p) cc_final: 0.7347 (t) REVERT: B 470 ASN cc_start: 0.7637 (m-40) cc_final: 0.7345 (m110) REVERT: B 477 LEU cc_start: 0.8605 (mp) cc_final: 0.8238 (tp) REVERT: B 480 ILE cc_start: 0.8113 (mt) cc_final: 0.7874 (mt) REVERT: B 490 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8587 (ttmt) REVERT: B 494 MET cc_start: 0.7587 (tpp) cc_final: 0.7252 (tpp) REVERT: B 500 ARG cc_start: 0.7966 (tmt-80) cc_final: 0.7407 (ttt-90) REVERT: B 506 ASN cc_start: 0.8486 (m-40) cc_final: 0.8266 (m-40) REVERT: B 512 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 517 PHE cc_start: 0.7161 (m-10) cc_final: 0.6625 (m-10) REVERT: B 580 GLU cc_start: 0.7180 (tp30) cc_final: 0.6496 (tp30) REVERT: B 583 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7228 (ttp-110) REVERT: B 586 MET cc_start: 0.7721 (tpt) cc_final: 0.7423 (tpt) REVERT: B 832 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 848 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 875 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7422 (ttp80) REVERT: B 877 GLN cc_start: 0.8309 (pp30) cc_final: 0.7864 (tm-30) REVERT: B 880 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7830 (ptpp) REVERT: B 899 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7136 (tmm-80) REVERT: B 902 ILE cc_start: 0.8786 (tt) cc_final: 0.8048 (tp) REVERT: B 903 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8051 (ttm170) REVERT: B 904 THR cc_start: 0.8239 (m) cc_final: 0.8019 (p) REVERT: B 906 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8370 (mm) REVERT: B 921 LEU cc_start: 0.8817 (tt) cc_final: 0.8544 (mm) REVERT: B 931 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 942 MET cc_start: 0.7884 (tpp) cc_final: 0.7622 (tpp) outliers start: 59 outliers final: 35 residues processed: 476 average time/residue: 0.2834 time to fit residues: 179.1855 Evaluate side-chains 506 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 456 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.0370 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10880 Z= 0.180 Angle : 0.680 14.239 14762 Z= 0.345 Chirality : 0.042 0.292 1782 Planarity : 0.004 0.033 1816 Dihedral : 5.790 59.343 1468 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.00 % Allowed : 26.55 % Favored : 68.45 % 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: 2.01 (0.23), residues: 1354 helix: 1.75 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 635 HIS 0.002 0.000 HIS B 614 PHE 0.026 0.001 PHE B 457 TYR 0.021 0.001 TYR B 594 ARG 0.006 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 449 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8286 (tptm) cc_final: 0.8052 (tptm) REVERT: A 103 THR cc_start: 0.8455 (p) cc_final: 0.8219 (p) REVERT: A 113 LEU cc_start: 0.8196 (tt) cc_final: 0.7954 (tp) REVERT: A 132 HIS cc_start: 0.6789 (m170) cc_final: 0.6554 (m170) REVERT: A 134 ASP cc_start: 0.7967 (t70) cc_final: 0.7680 (t0) REVERT: A 138 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 154 MET cc_start: 0.7258 (tpp) cc_final: 0.6928 (tpp) REVERT: A 155 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6120 (p0) REVERT: A 158 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7399 (p) REVERT: A 161 ARG cc_start: 0.7534 (mmt180) cc_final: 0.7193 (mmt180) REVERT: A 199 MET cc_start: 0.7880 (tpt) cc_final: 0.7646 (tpp) REVERT: A 204 ILE cc_start: 0.8675 (mt) cc_final: 0.8335 (tt) REVERT: A 206 SER cc_start: 0.8226 (t) cc_final: 0.7423 (p) REVERT: A 233 GLU cc_start: 0.8287 (tt0) cc_final: 0.7939 (tt0) REVERT: A 237 ASN cc_start: 0.8115 (t0) cc_final: 0.7545 (t0) REVERT: A 238 ASP cc_start: 0.7164 (m-30) cc_final: 0.6711 (m-30) REVERT: A 248 PHE cc_start: 0.8039 (m-80) cc_final: 0.7410 (m-10) REVERT: A 252 VAL cc_start: 0.7146 (t) cc_final: 0.6506 (m) REVERT: A 278 TRP cc_start: 0.8370 (t-100) cc_final: 0.7848 (t-100) REVERT: A 293 ILE cc_start: 0.8669 (mm) cc_final: 0.8195 (mm) REVERT: A 312 TYR cc_start: 0.8234 (t80) cc_final: 0.7729 (t80) REVERT: A 316 ASP cc_start: 0.7404 (m-30) cc_final: 0.6855 (m-30) REVERT: A 345 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (m) REVERT: A 351 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7917 (tpp80) REVERT: A 364 ILE cc_start: 0.7978 (mt) cc_final: 0.7573 (tt) REVERT: A 384 ASP cc_start: 0.8137 (t0) cc_final: 0.7862 (t0) REVERT: A 393 LEU cc_start: 0.8807 (mp) cc_final: 0.8346 (mp) REVERT: A 396 THR cc_start: 0.8280 (m) cc_final: 0.8006 (p) REVERT: A 401 MET cc_start: 0.7695 (ttm) cc_final: 0.7454 (ttm) REVERT: A 420 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7475 (mtm-85) REVERT: A 425 MET cc_start: 0.8231 (tpt) cc_final: 0.7602 (tpp) REVERT: A 443 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 444 ASN cc_start: 0.8304 (t0) cc_final: 0.8081 (t0) REVERT: A 449 ASP cc_start: 0.8426 (t0) cc_final: 0.8174 (t0) REVERT: A 466 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 475 GLN cc_start: 0.8569 (tp40) cc_final: 0.8275 (mm-40) REVERT: A 485 ASP cc_start: 0.8038 (t0) cc_final: 0.7632 (t0) REVERT: A 486 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 494 MET cc_start: 0.8066 (tpp) cc_final: 0.7464 (tpp) REVERT: A 499 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7854 (ttp80) REVERT: A 500 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7947 (ttt180) REVERT: A 501 ILE cc_start: 0.8702 (tt) cc_final: 0.8452 (pt) REVERT: A 505 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 506 ASN cc_start: 0.8462 (m-40) cc_final: 0.8003 (m-40) REVERT: A 507 ARG cc_start: 0.8171 (ptp-110) cc_final: 0.7881 (ptp-110) REVERT: A 511 MET cc_start: 0.8212 (ttm) cc_final: 0.7609 (tmm) REVERT: A 517 PHE cc_start: 0.8200 (m-10) cc_final: 0.7935 (m-80) REVERT: A 532 ILE cc_start: 0.8055 (mm) cc_final: 0.7739 (mm) REVERT: A 585 ARG cc_start: 0.8488 (tmm-80) cc_final: 0.8222 (tmm-80) REVERT: A 586 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7456 (ptm) REVERT: A 587 LEU cc_start: 0.8852 (pp) cc_final: 0.8247 (pp) REVERT: A 590 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 591 LYS cc_start: 0.8652 (pttp) cc_final: 0.8311 (pttp) REVERT: A 600 HIS cc_start: 0.7813 (t70) cc_final: 0.7386 (t70) REVERT: A 610 LEU cc_start: 0.8843 (tt) cc_final: 0.8077 (tp) REVERT: A 613 GLN cc_start: 0.8558 (pp30) cc_final: 0.7900 (pp30) REVERT: A 647 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8531 (mtmt) REVERT: A 832 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 841 LYS cc_start: 0.8746 (mptt) cc_final: 0.8357 (tptt) REVERT: A 844 ILE cc_start: 0.9059 (mm) cc_final: 0.8519 (mt) REVERT: A 847 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7937 (mp0) REVERT: A 848 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 857 MET cc_start: 0.7899 (ppp) cc_final: 0.7549 (ppp) REVERT: A 866 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6416 (tm-30) REVERT: A 875 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7343 (ttp80) REVERT: A 888 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 897 LYS cc_start: 0.8662 (pttt) cc_final: 0.8260 (pttt) REVERT: A 899 ARG cc_start: 0.7748 (mtt90) cc_final: 0.7365 (mtt90) REVERT: A 906 LEU cc_start: 0.8366 (mt) cc_final: 0.7996 (mm) REVERT: A 908 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7512 (t-90) REVERT: A 909 SER cc_start: 0.8707 (t) cc_final: 0.8478 (p) REVERT: A 911 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6956 (mt-10) REVERT: A 923 ASP cc_start: 0.5701 (p0) cc_final: 0.5347 (p0) REVERT: A 938 MET cc_start: 0.8345 (tpp) cc_final: 0.8036 (tpp) REVERT: B 92 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8480 (mtp85) REVERT: B 112 ILE cc_start: 0.8157 (mt) cc_final: 0.7875 (mm) REVERT: B 156 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8338 (t) REVERT: B 163 PHE cc_start: 0.8134 (t80) cc_final: 0.7618 (t80) REVERT: B 166 VAL cc_start: 0.8509 (t) cc_final: 0.8181 (p) REVERT: B 189 PHE cc_start: 0.7861 (m-10) cc_final: 0.7389 (m-10) REVERT: B 191 TYR cc_start: 0.8582 (m-80) cc_final: 0.8314 (m-80) REVERT: B 199 MET cc_start: 0.7565 (tpt) cc_final: 0.6941 (tpp) REVERT: B 205 MET cc_start: 0.8063 (tpp) cc_final: 0.7800 (mmp) REVERT: B 218 LYS cc_start: 0.8492 (ptmm) cc_final: 0.8126 (ptmm) REVERT: B 233 GLU cc_start: 0.7824 (tt0) cc_final: 0.7540 (tm-30) REVERT: B 237 ASN cc_start: 0.7881 (t0) cc_final: 0.7670 (t0) REVERT: B 242 ILE cc_start: 0.8491 (mt) cc_final: 0.8223 (mm) REVERT: B 251 MET cc_start: 0.6798 (tmm) cc_final: 0.6484 (tmm) REVERT: B 263 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 293 ILE cc_start: 0.8503 (mt) cc_final: 0.8259 (tp) REVERT: B 337 GLU cc_start: 0.7300 (tp30) cc_final: 0.6950 (mm-30) REVERT: B 344 GLU cc_start: 0.7566 (pp20) cc_final: 0.7322 (pp20) REVERT: B 366 MET cc_start: 0.7613 (ttm) cc_final: 0.7409 (mtm) REVERT: B 375 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7842 (ptpt) REVERT: B 383 MET cc_start: 0.7280 (tpp) cc_final: 0.5943 (tpp) REVERT: B 386 PHE cc_start: 0.7710 (t80) cc_final: 0.7325 (t80) REVERT: B 387 TYR cc_start: 0.7755 (m-10) cc_final: 0.7367 (m-80) REVERT: B 393 LEU cc_start: 0.8598 (mp) cc_final: 0.8270 (mp) REVERT: B 396 THR cc_start: 0.8419 (m) cc_final: 0.7965 (p) REVERT: B 397 ILE cc_start: 0.8655 (mt) cc_final: 0.8266 (mm) REVERT: B 406 PHE cc_start: 0.8293 (m-80) cc_final: 0.8060 (m-80) REVERT: B 413 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.4724 (mp) REVERT: B 424 ILE cc_start: 0.8842 (tp) cc_final: 0.8596 (tp) REVERT: B 444 ASN cc_start: 0.8027 (t0) cc_final: 0.7792 (t0) REVERT: B 445 LEU cc_start: 0.8462 (tp) cc_final: 0.8211 (tp) REVERT: B 466 THR cc_start: 0.7605 (p) cc_final: 0.7335 (t) REVERT: B 470 ASN cc_start: 0.7633 (m-40) cc_final: 0.7357 (m110) REVERT: B 475 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7937 (tp40) REVERT: B 477 LEU cc_start: 0.8591 (mp) cc_final: 0.8223 (tp) REVERT: B 480 ILE cc_start: 0.8066 (mt) cc_final: 0.7843 (mt) REVERT: B 490 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8623 (ttmt) REVERT: B 494 MET cc_start: 0.7559 (tpp) cc_final: 0.7266 (tpp) REVERT: B 500 ARG cc_start: 0.7911 (tmt-80) cc_final: 0.7308 (ttt-90) REVERT: B 506 ASN cc_start: 0.8480 (m-40) cc_final: 0.8273 (m-40) REVERT: B 512 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 517 PHE cc_start: 0.7079 (m-10) cc_final: 0.6396 (m-10) REVERT: B 531 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7613 (tp30) REVERT: B 586 MET cc_start: 0.7767 (tpt) cc_final: 0.7268 (tpt) REVERT: B 594 TYR cc_start: 0.7984 (m-80) cc_final: 0.7567 (m-80) REVERT: B 832 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 833 LEU cc_start: 0.8786 (tt) cc_final: 0.8361 (pp) REVERT: B 848 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 877 GLN cc_start: 0.8137 (pp30) cc_final: 0.7662 (tp40) REVERT: B 880 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7806 (ptpp) REVERT: B 881 GLU cc_start: 0.7912 (pt0) cc_final: 0.7337 (pt0) REVERT: B 899 ARG cc_start: 0.7874 (tmm-80) cc_final: 0.7184 (tmm-80) REVERT: B 902 ILE cc_start: 0.8775 (tt) cc_final: 0.8025 (tp) REVERT: B 903 ARG cc_start: 0.8464 (ttm170) cc_final: 0.7932 (mtm110) REVERT: B 904 THR cc_start: 0.8217 (m) cc_final: 0.7992 (p) REVERT: B 906 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8383 (mm) REVERT: B 921 LEU cc_start: 0.8778 (tt) cc_final: 0.8411 (mp) REVERT: B 926 GLU cc_start: 0.7595 (mp0) cc_final: 0.7276 (mm-30) REVERT: B 931 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 942 MET cc_start: 0.7879 (tpp) cc_final: 0.7623 (tpp) outliers start: 58 outliers final: 40 residues processed: 467 average time/residue: 0.2747 time to fit residues: 170.7666 Evaluate side-chains 497 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 444 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5263 > 50: distance: 41 - 46: 15.936 distance: 46 - 47: 21.396 distance: 47 - 48: 23.683 distance: 47 - 50: 24.053 distance: 48 - 49: 30.384 distance: 48 - 60: 24.047 distance: 50 - 51: 6.805 distance: 51 - 52: 23.540 distance: 51 - 53: 21.058 distance: 52 - 54: 9.946 distance: 53 - 55: 3.562 distance: 53 - 56: 15.087 distance: 54 - 55: 10.073 distance: 55 - 57: 13.040 distance: 57 - 59: 13.394 distance: 58 - 59: 14.597 distance: 60 - 61: 6.939 distance: 61 - 62: 19.001 distance: 61 - 64: 23.634 distance: 62 - 68: 6.917 distance: 63 - 94: 56.444 distance: 64 - 65: 14.024 distance: 65 - 67: 21.293 distance: 68 - 69: 18.502 distance: 69 - 70: 22.289 distance: 69 - 72: 11.481 distance: 70 - 71: 18.104 distance: 70 - 79: 9.989 distance: 71 - 99: 30.325 distance: 72 - 73: 15.673 distance: 73 - 74: 14.138 distance: 73 - 75: 31.966 distance: 74 - 76: 38.728 distance: 75 - 77: 24.432 distance: 76 - 78: 24.835 distance: 77 - 78: 13.279 distance: 79 - 80: 16.470 distance: 80 - 81: 6.067 distance: 80 - 83: 9.807 distance: 81 - 82: 10.369 distance: 81 - 85: 11.024 distance: 82 - 107: 31.326 distance: 83 - 84: 22.927 distance: 85 - 86: 20.863 distance: 86 - 87: 9.404 distance: 86 - 89: 14.161 distance: 87 - 88: 20.472 distance: 87 - 94: 6.046 distance: 88 - 115: 28.713 distance: 89 - 90: 35.145 distance: 90 - 91: 16.118 distance: 91 - 92: 11.252 distance: 91 - 93: 19.293 distance: 94 - 95: 10.553 distance: 95 - 96: 17.459 distance: 95 - 98: 19.382 distance: 96 - 97: 9.989 distance: 96 - 99: 7.570 distance: 97 - 126: 38.983 distance: 99 - 100: 18.684 distance: 100 - 101: 6.035 distance: 100 - 103: 6.519 distance: 101 - 102: 19.195 distance: 101 - 107: 15.212 distance: 102 - 130: 19.953 distance: 103 - 104: 14.185 distance: 104 - 105: 16.942 distance: 105 - 106: 24.074 distance: 107 - 108: 10.678 distance: 108 - 109: 8.881 distance: 108 - 111: 11.120 distance: 109 - 110: 15.572 distance: 109 - 115: 11.203 distance: 110 - 135: 8.608 distance: 111 - 112: 11.208 distance: 112 - 113: 9.174 distance: 113 - 114: 18.228 distance: 115 - 116: 5.604 distance: 116 - 117: 9.935 distance: 116 - 119: 10.800 distance: 117 - 118: 8.374 distance: 117 - 126: 9.689 distance: 118 - 143: 20.821 distance: 119 - 120: 14.445 distance: 120 - 121: 10.215 distance: 120 - 122: 12.181 distance: 121 - 123: 7.210 distance: 122 - 124: 14.631 distance: 123 - 125: 6.815 distance: 124 - 125: 14.564 distance: 126 - 127: 8.459 distance: 127 - 128: 4.732 distance: 128 - 129: 12.015 distance: 128 - 130: 12.445 distance: 129 - 151: 24.646