Starting phenix.real_space_refine on Wed Jan 15 05:26:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.map" model { file = "/net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v12_42878/01_2025/8v12_42878.cif" } resolution = 3.81 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= 0.020 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 44 5.16 5 C 5231 2.51 5 N 1243 2.21 5 O 1442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7918 Classifications: {'peptide': 979} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 953} Chain breaks: 5 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'TYR:plan': 2, 'HIS%COO:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.64 Number of scatterers: 7960 At special positions: 0 Unit cell: (89.88, 97.37, 127.33, 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 44 16.00 O 1442 8.00 N 1243 7.00 C 5231 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 Links applied NAG-ASN " NAG A1502 " - " ASN A 165 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 850.1 milliseconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 70.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 3 through 35 removed outlier: 3.706A pdb=" N ARG A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.764A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 103 through 120 Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.767A pdb=" N TYR A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.593A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.572A pdb=" N ALA A 337 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.510A pdb=" N GLY A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.667A pdb=" N ILE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 493 through 516 Processing helix chain 'A' and resid 524 through 550 removed outlier: 3.699A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.620A pdb=" N ASP A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 619 removed outlier: 3.803A pdb=" N ALA A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 660 removed outlier: 3.574A pdb=" N LEU A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 722 through 736 Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1067 through 1074 Processing helix chain 'A' and resid 1074 through 1099 Processing helix chain 'A' and resid 1113 through 1126 Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'A' and resid 1184 through 1201 Processing helix chain 'A' and resid 1209 through 1218 removed outlier: 3.612A pdb=" N PHE A1213 " --> pdb=" O ASN A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 removed outlier: 4.045A pdb=" N LYS A1224 " --> pdb=" O SER A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1240 Processing helix chain 'A' and resid 1241 through 1247 Processing helix chain 'A' and resid 1272 through 1287 Processing helix chain 'A' and resid 1289 through 1293 removed outlier: 3.606A pdb=" N HIS A1292 " --> pdb=" O LEU A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1333 removed outlier: 5.199A pdb=" N ILE A1313 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU A1314 " --> pdb=" O GLU A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1362 Processing helix chain 'A' and resid 1367 through 1395 removed outlier: 3.579A pdb=" N VAL A1375 " --> pdb=" O MET A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1428 removed outlier: 5.952A pdb=" N GLY A1413 " --> pdb=" O HIS A1409 " (cutoff:3.500A) Proline residue: A1414 - end of helix removed outlier: 4.474A pdb=" N THR A1428 " --> pdb=" O PHE A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1431 No H-bonds generated for 'chain 'A' and resid 1429 through 1431' Processing helix chain 'A' and resid 1434 through 1457 removed outlier: 3.537A pdb=" N VAL A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A1440 " --> pdb=" O PHE A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.632A pdb=" N ALA A 420 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET A 406 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 304 removed outlier: 4.051A pdb=" N ALA A1260 " --> pdb=" O VAL A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 304 removed outlier: 4.051A pdb=" N ALA A1260 " --> pdb=" O VAL A1252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 390 removed outlier: 4.023A pdb=" N TYR A 388 " --> pdb=" O MET A 397 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1488 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: 2.75 Time building geometry restraints manager: 2.58 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: 2420 1.34 - 1.46: 1864 1.46 - 1.58: 3797 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 8147 Sorted by residual: bond pdb=" N THR A 117 " pdb=" CA THR A 117 " ideal model delta sigma weight residual 1.459 1.443 0.017 1.19e-02 7.06e+03 1.92e+00 bond pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.27e-02 6.20e+03 1.74e+00 bond pdb=" CA TYR A 449 " pdb=" C TYR A 449 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.30e-02 5.92e+03 1.58e+00 bond pdb=" CA ASP A 448 " pdb=" C ASP A 448 " ideal model delta sigma weight residual 1.523 1.508 0.016 1.30e-02 5.92e+03 1.46e+00 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.38e+00 ... (remaining 8142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 10797 1.48 - 2.96: 195 2.96 - 4.43: 21 4.43 - 5.91: 5 5.91 - 7.39: 2 Bond angle restraints: 11020 Sorted by residual: angle pdb=" N LYS A 112 " pdb=" CA LYS A 112 " pdb=" C LYS A 112 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.65e+01 angle pdb=" N THR A 117 " pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 111.07 107.85 3.22 1.07e+00 8.73e-01 9.06e+00 angle pdb=" N ASP A 448 " pdb=" CA ASP A 448 " pdb=" C ASP A 448 " ideal model delta sigma weight residual 111.28 108.25 3.03 1.09e+00 8.42e-01 7.71e+00 angle pdb=" N THR A 645 " pdb=" CA THR A 645 " pdb=" C THR A 645 " ideal model delta sigma weight residual 112.93 109.47 3.46 1.33e+00 5.65e-01 6.78e+00 angle pdb=" N LEU A 446 " pdb=" CA LEU A 446 " pdb=" C LEU A 446 " ideal model delta sigma weight residual 111.07 113.78 -2.71 1.07e+00 8.73e-01 6.40e+00 ... (remaining 11015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 4680 21.41 - 42.82: 171 42.82 - 64.24: 15 64.24 - 85.65: 1 85.65 - 107.06: 8 Dihedral angle restraints: 4875 sinusoidal: 1980 harmonic: 2895 Sorted by residual: dihedral pdb=" C1 NAG A1502 " pdb=" C2 NAG A1502 " pdb=" C3 NAG A1502 " pdb=" O3 NAG A1502 " ideal model delta sinusoidal sigma weight residual -175.09 -68.03 -107.06 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C1 NAG A1502 " pdb=" C2 NAG A1502 " pdb=" C3 NAG A1502 " pdb=" C4 NAG A1502 " ideal model delta sinusoidal sigma weight residual -52.39 54.21 -106.60 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" N2 NAG A1502 " pdb=" C2 NAG A1502 " pdb=" C3 NAG A1502 " pdb=" O3 NAG A1502 " ideal model delta sinusoidal sigma weight residual 62.25 168.21 -105.96 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 859 0.029 - 0.059: 240 0.059 - 0.088: 112 0.088 - 0.118: 39 0.118 - 0.147: 4 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" C1 NAG A1502 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1502 " pdb=" O5 NAG A1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE A 380 " pdb=" N ILE A 380 " pdb=" C ILE A 380 " pdb=" CB ILE A 380 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1251 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1143 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C ILE A1143 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE A1143 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A1144 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 574 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C VAL A 574 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL A 574 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 575 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 565 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ILE A 565 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 565 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 566 " -0.008 2.00e-02 2.50e+03 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 568 2.74 - 3.28: 9077 3.28 - 3.82: 14585 3.82 - 4.36: 16918 4.36 - 4.90: 27637 Nonbonded interactions: 68785 Sorted by model distance: nonbonded pdb=" O TYR A 64 " pdb=" OG SER A 68 " model vdw 2.196 3.040 nonbonded pdb=" O ASN A1367 " pdb=" OG SER A1370 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 478 " pdb=" OG SER A 481 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG SER A 125 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 155 " pdb=" O TYR A 306 " model vdw 2.284 3.040 ... (remaining 68780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.002 0.030 8147 Z= 0.153 Angle : 0.502 7.389 11020 Z= 0.315 Chirality : 0.036 0.147 1254 Planarity : 0.003 0.034 1361 Dihedral : 11.584 107.060 3007 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.72 % Allowed : 7.26 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.07 (0.27), residues: 967 helix: 2.38 (0.21), residues: 609 sheet: -1.76 (0.78), residues: 36 loop : -0.20 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1423 HIS 0.005 0.001 HIS A 8 PHE 0.012 0.001 PHE A 646 TYR 0.013 0.001 TYR A 521 ARG 0.002 0.000 ARG A1117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 317 time to evaluate : 0.906 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: A 38 THR cc_start: 0.7362 (p) cc_final: 0.6963 (m) REVERT: A 169 PHE cc_start: 0.6826 (m-10) cc_final: 0.5672 (m-80) REVERT: A 352 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7998 (pp) REVERT: A 727 ILE cc_start: 0.8567 (tp) cc_final: 0.8099 (tt) REVERT: A 728 HIS cc_start: 0.6987 (t70) cc_final: 0.6455 (t-170) REVERT: A 1420 LEU cc_start: 0.7708 (mt) cc_final: 0.7259 (mt) outliers start: 24 outliers final: 4 residues processed: 334 average time/residue: 0.1872 time to fit residues: 86.0408 Evaluate side-chains 206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 1312 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 344 GLN A 433 HIS A 514 ASN A 588 ASN A 593 GLN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 ASN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.084840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071349 restraints weight = 32686.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073465 restraints weight = 19641.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.074978 restraints weight = 13783.595| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8147 Z= 0.217 Angle : 0.664 8.280 11020 Z= 0.345 Chirality : 0.047 0.295 1254 Planarity : 0.004 0.045 1361 Dihedral : 8.337 78.434 1152 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 14.40 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.80 (0.26), residues: 967 helix: 2.08 (0.20), residues: 610 sheet: -1.58 (0.80), residues: 42 loop : -0.10 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1237 HIS 0.010 0.002 HIS A 8 PHE 0.021 0.002 PHE A1454 TYR 0.019 0.002 TYR A 442 ARG 0.006 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.964 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: A 105 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9039 (mmmt) REVERT: A 169 PHE cc_start: 0.8023 (m-10) cc_final: 0.6852 (m-80) REVERT: A 334 LEU cc_start: 0.8818 (mm) cc_final: 0.8580 (mm) REVERT: A 352 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8964 (pp) REVERT: A 424 MET cc_start: 0.8396 (tpp) cc_final: 0.8115 (tpp) REVERT: A 452 PHE cc_start: 0.9445 (m-10) cc_final: 0.9108 (m-80) REVERT: A 573 PHE cc_start: 0.8806 (m-80) cc_final: 0.8357 (m-80) REVERT: A 611 ILE cc_start: 0.9393 (mt) cc_final: 0.9191 (mm) REVERT: A 724 TYR cc_start: 0.8825 (m-80) cc_final: 0.8618 (m-80) REVERT: A 726 TRP cc_start: 0.8809 (t60) cc_final: 0.8481 (t60) REVERT: A 728 HIS cc_start: 0.8579 (t70) cc_final: 0.8187 (t70) REVERT: A 1099 MET cc_start: 0.5409 (ptp) cc_final: 0.5066 (tpp) REVERT: A 1191 LEU cc_start: 0.9204 (mt) cc_final: 0.8990 (mt) REVERT: A 1232 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8841 (mm-30) REVERT: A 1296 MET cc_start: 0.8876 (mmm) cc_final: 0.7529 (mmm) REVERT: A 1356 PHE cc_start: 0.8514 (t80) cc_final: 0.8101 (t80) REVERT: A 1384 HIS cc_start: 0.9109 (m90) cc_final: 0.8648 (m90) REVERT: A 1396 MET cc_start: 0.7243 (tpt) cc_final: 0.6827 (mmm) REVERT: A 1420 LEU cc_start: 0.9300 (mt) cc_final: 0.8965 (mt) REVERT: A 1458 PHE cc_start: 0.9057 (t80) cc_final: 0.8853 (t80) outliers start: 37 outliers final: 12 residues processed: 247 average time/residue: 0.1792 time to fit residues: 61.9884 Evaluate side-chains 197 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1435 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.085102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071236 restraints weight = 33975.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.073408 restraints weight = 20380.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.074980 restraints weight = 14248.910| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8147 Z= 0.212 Angle : 0.682 13.124 11020 Z= 0.347 Chirality : 0.046 0.267 1254 Planarity : 0.004 0.051 1361 Dihedral : 7.026 74.788 1144 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.85 % Allowed : 17.23 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.67 (0.26), residues: 967 helix: 1.91 (0.20), residues: 611 sheet: -0.97 (0.93), residues: 36 loop : -0.14 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1423 HIS 0.009 0.001 HIS A 8 PHE 0.039 0.002 PHE A1424 TYR 0.017 0.002 TYR A 75 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.998 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: A 112 LYS cc_start: 0.9344 (mttm) cc_final: 0.9038 (mttm) REVERT: A 169 PHE cc_start: 0.8017 (m-10) cc_final: 0.6814 (m-80) REVERT: A 334 LEU cc_start: 0.8733 (mm) cc_final: 0.8492 (mm) REVERT: A 352 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8980 (pp) REVERT: A 424 MET cc_start: 0.8533 (tpp) cc_final: 0.8270 (tpp) REVERT: A 573 PHE cc_start: 0.8838 (m-80) cc_final: 0.8481 (m-80) REVERT: A 594 MET cc_start: 0.8711 (mmt) cc_final: 0.8431 (mmm) REVERT: A 642 MET cc_start: 0.8510 (mtp) cc_final: 0.8302 (ttm) REVERT: A 724 TYR cc_start: 0.8849 (m-80) cc_final: 0.8599 (m-80) REVERT: A 728 HIS cc_start: 0.8586 (t70) cc_final: 0.8261 (t70) REVERT: A 1088 ILE cc_start: 0.9591 (mm) cc_final: 0.9373 (mm) REVERT: A 1099 MET cc_start: 0.5480 (ptp) cc_final: 0.4981 (tpt) REVERT: A 1232 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8850 (mm-30) REVERT: A 1266 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (t80) REVERT: A 1296 MET cc_start: 0.8849 (mmm) cc_final: 0.7645 (mmm) REVERT: A 1317 LEU cc_start: 0.9020 (tt) cc_final: 0.8814 (pp) REVERT: A 1319 ASN cc_start: 0.9048 (m-40) cc_final: 0.8773 (m110) REVERT: A 1328 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 1356 PHE cc_start: 0.8461 (t80) cc_final: 0.8215 (t80) REVERT: A 1384 HIS cc_start: 0.9086 (m90) cc_final: 0.8370 (m90) REVERT: A 1396 MET cc_start: 0.7414 (tpt) cc_final: 0.6986 (mmm) REVERT: A 1420 LEU cc_start: 0.9301 (mt) cc_final: 0.9087 (mt) REVERT: A 1458 PHE cc_start: 0.8949 (t80) cc_final: 0.8723 (t80) outliers start: 34 outliers final: 20 residues processed: 225 average time/residue: 0.1752 time to fit residues: 55.6636 Evaluate side-chains 207 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.084917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071070 restraints weight = 33629.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073147 restraints weight = 20352.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074688 restraints weight = 14350.680| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8147 Z= 0.203 Angle : 0.668 16.017 11020 Z= 0.336 Chirality : 0.045 0.250 1254 Planarity : 0.004 0.050 1361 Dihedral : 6.342 74.693 1144 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.88 % Allowed : 17.57 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.65 (0.27), residues: 967 helix: 1.94 (0.20), residues: 607 sheet: -1.14 (1.36), residues: 21 loop : -0.27 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1279 HIS 0.005 0.001 HIS A1417 PHE 0.045 0.001 PHE A1424 TYR 0.013 0.002 TYR A1265 ARG 0.004 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.870 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: A 13 LEU cc_start: 0.9084 (pp) cc_final: 0.8657 (mm) REVERT: A 50 LEU cc_start: 0.9181 (mm) cc_final: 0.8788 (tp) REVERT: A 60 GLU cc_start: 0.6991 (tp30) cc_final: 0.6745 (tp30) REVERT: A 94 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 108 ARG cc_start: 0.9066 (mtt-85) cc_final: 0.8814 (mtt-85) REVERT: A 169 PHE cc_start: 0.8087 (m-10) cc_final: 0.6927 (m-80) REVERT: A 334 LEU cc_start: 0.8770 (mm) cc_final: 0.8519 (mm) REVERT: A 352 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8940 (pp) REVERT: A 424 MET cc_start: 0.8591 (tpp) cc_final: 0.8330 (tpp) REVERT: A 458 ILE cc_start: 0.8466 (tp) cc_final: 0.7510 (tp) REVERT: A 594 MET cc_start: 0.8740 (mmt) cc_final: 0.8406 (mmm) REVERT: A 642 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8238 (ttm) REVERT: A 724 TYR cc_start: 0.8867 (m-80) cc_final: 0.8455 (m-80) REVERT: A 728 HIS cc_start: 0.8742 (t70) cc_final: 0.8341 (t-170) REVERT: A 1084 MET cc_start: 0.8926 (ptp) cc_final: 0.8609 (ptp) REVERT: A 1088 ILE cc_start: 0.9621 (mm) cc_final: 0.9379 (mm) REVERT: A 1099 MET cc_start: 0.5661 (ptp) cc_final: 0.5148 (tpt) REVERT: A 1134 GLU cc_start: 0.8992 (pt0) cc_final: 0.8186 (pm20) REVERT: A 1232 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8852 (mm-30) REVERT: A 1266 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8493 (t80) REVERT: A 1296 MET cc_start: 0.8761 (mmm) cc_final: 0.7577 (mmm) REVERT: A 1317 LEU cc_start: 0.9042 (tt) cc_final: 0.8792 (pp) REVERT: A 1319 ASN cc_start: 0.9077 (m-40) cc_final: 0.8814 (m110) REVERT: A 1328 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 1384 HIS cc_start: 0.9091 (m90) cc_final: 0.8516 (m90) REVERT: A 1396 MET cc_start: 0.7357 (tpt) cc_final: 0.6856 (mmm) REVERT: A 1420 LEU cc_start: 0.9288 (mt) cc_final: 0.9087 (mt) REVERT: A 1458 PHE cc_start: 0.8997 (t80) cc_final: 0.8699 (t80) outliers start: 43 outliers final: 24 residues processed: 220 average time/residue: 0.1753 time to fit residues: 54.5973 Evaluate side-chains 204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.085059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071182 restraints weight = 33351.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.073298 restraints weight = 20060.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074806 restraints weight = 14190.214| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8147 Z= 0.208 Angle : 0.689 17.028 11020 Z= 0.341 Chirality : 0.045 0.310 1254 Planarity : 0.004 0.052 1361 Dihedral : 5.963 74.496 1144 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.31 % Allowed : 18.93 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.64 (0.27), residues: 967 helix: 1.87 (0.20), residues: 613 sheet: -1.27 (1.33), residues: 21 loop : -0.16 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 726 HIS 0.004 0.001 HIS A 475 PHE 0.041 0.002 PHE A1424 TYR 0.022 0.002 TYR A 408 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.6909 (tp30) cc_final: 0.6579 (tp30) REVERT: A 82 ASN cc_start: 0.9206 (m-40) cc_final: 0.8911 (m110) REVERT: A 108 ARG cc_start: 0.9082 (mtt-85) cc_final: 0.8734 (mtt-85) REVERT: A 112 LYS cc_start: 0.9268 (mttm) cc_final: 0.9000 (mttm) REVERT: A 169 PHE cc_start: 0.8158 (m-10) cc_final: 0.7044 (m-80) REVERT: A 352 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 424 MET cc_start: 0.8646 (tpp) cc_final: 0.8371 (tpp) REVERT: A 594 MET cc_start: 0.8739 (mmt) cc_final: 0.8377 (mmm) REVERT: A 596 LEU cc_start: 0.9104 (tp) cc_final: 0.8797 (tp) REVERT: A 642 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: A 724 TYR cc_start: 0.8870 (m-80) cc_final: 0.8366 (m-80) REVERT: A 728 HIS cc_start: 0.8713 (t70) cc_final: 0.8320 (t-170) REVERT: A 1088 ILE cc_start: 0.9630 (mm) cc_final: 0.9313 (mm) REVERT: A 1099 MET cc_start: 0.5724 (ptp) cc_final: 0.5275 (tpt) REVERT: A 1116 ARG cc_start: 0.8451 (tpt170) cc_final: 0.8147 (tpt170) REVERT: A 1232 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8845 (mm-30) REVERT: A 1266 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8484 (t80) REVERT: A 1317 LEU cc_start: 0.9020 (tt) cc_final: 0.8792 (pp) REVERT: A 1319 ASN cc_start: 0.9058 (m-40) cc_final: 0.8780 (m110) REVERT: A 1328 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 1384 HIS cc_start: 0.9125 (m90) cc_final: 0.8766 (m90) REVERT: A 1396 MET cc_start: 0.7314 (tpt) cc_final: 0.6803 (mmm) REVERT: A 1458 PHE cc_start: 0.8931 (t80) cc_final: 0.8559 (t80) outliers start: 38 outliers final: 23 residues processed: 214 average time/residue: 0.1726 time to fit residues: 52.5251 Evaluate side-chains 201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.086240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072296 restraints weight = 32979.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.074423 restraints weight = 20048.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.075911 restraints weight = 14192.483| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8147 Z= 0.193 Angle : 0.711 17.271 11020 Z= 0.348 Chirality : 0.046 0.282 1254 Planarity : 0.004 0.051 1361 Dihedral : 5.785 74.568 1144 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.31 % Allowed : 20.86 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.61 (0.27), residues: 967 helix: 1.83 (0.20), residues: 616 sheet: -1.55 (1.11), residues: 27 loop : -0.11 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 726 HIS 0.004 0.001 HIS A 475 PHE 0.042 0.002 PHE A1424 TYR 0.016 0.002 TYR A 408 ARG 0.009 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.6975 (tp30) cc_final: 0.6596 (tp30) REVERT: A 82 ASN cc_start: 0.9204 (m-40) cc_final: 0.8900 (m110) REVERT: A 94 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 103 LYS cc_start: 0.9105 (tppt) cc_final: 0.8511 (tppt) REVERT: A 169 PHE cc_start: 0.8163 (m-10) cc_final: 0.7054 (m-80) REVERT: A 352 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 424 MET cc_start: 0.8674 (tpp) cc_final: 0.8386 (tpp) REVERT: A 594 MET cc_start: 0.8707 (mmt) cc_final: 0.8340 (mmm) REVERT: A 596 LEU cc_start: 0.9069 (tp) cc_final: 0.8755 (tp) REVERT: A 642 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8191 (ttm) REVERT: A 724 TYR cc_start: 0.8851 (m-80) cc_final: 0.8321 (m-80) REVERT: A 728 HIS cc_start: 0.8724 (t70) cc_final: 0.8329 (t-170) REVERT: A 1088 ILE cc_start: 0.9575 (mm) cc_final: 0.9277 (mm) REVERT: A 1099 MET cc_start: 0.5558 (ptp) cc_final: 0.5114 (tpt) REVERT: A 1232 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8832 (mm-30) REVERT: A 1266 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 1317 LEU cc_start: 0.9008 (tt) cc_final: 0.8782 (pp) REVERT: A 1319 ASN cc_start: 0.9015 (m-40) cc_final: 0.8743 (m110) REVERT: A 1384 HIS cc_start: 0.9133 (m90) cc_final: 0.8769 (m90) REVERT: A 1396 MET cc_start: 0.7294 (tpt) cc_final: 0.6757 (mmm) REVERT: A 1458 PHE cc_start: 0.8956 (t80) cc_final: 0.8520 (t80) outliers start: 38 outliers final: 21 residues processed: 210 average time/residue: 0.1752 time to fit residues: 53.2762 Evaluate side-chains 198 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.086291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.072201 restraints weight = 33315.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074356 restraints weight = 20072.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.075864 restraints weight = 14211.153| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8147 Z= 0.207 Angle : 0.740 17.819 11020 Z= 0.360 Chirality : 0.046 0.316 1254 Planarity : 0.004 0.046 1361 Dihedral : 5.531 74.728 1144 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.97 % Allowed : 21.88 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.62 (0.27), residues: 967 helix: 1.83 (0.20), residues: 618 sheet: -1.33 (1.12), residues: 27 loop : -0.10 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 726 HIS 0.004 0.001 HIS A 475 PHE 0.047 0.002 PHE A1424 TYR 0.014 0.001 TYR A 408 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9173 (mm) cc_final: 0.8800 (tp) REVERT: A 60 GLU cc_start: 0.6913 (tp30) cc_final: 0.6654 (tp30) REVERT: A 94 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8793 (tt) REVERT: A 169 PHE cc_start: 0.8185 (m-10) cc_final: 0.6998 (m-80) REVERT: A 352 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8919 (pp) REVERT: A 424 MET cc_start: 0.8726 (tpp) cc_final: 0.8428 (tpp) REVERT: A 482 LEU cc_start: 0.9426 (pp) cc_final: 0.9178 (tp) REVERT: A 594 MET cc_start: 0.8628 (mmt) cc_final: 0.8242 (mmm) REVERT: A 596 LEU cc_start: 0.9064 (tp) cc_final: 0.8797 (tp) REVERT: A 623 TYR cc_start: 0.7871 (t80) cc_final: 0.7387 (t80) REVERT: A 642 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8212 (ttm) REVERT: A 724 TYR cc_start: 0.8868 (m-80) cc_final: 0.8337 (m-80) REVERT: A 728 HIS cc_start: 0.8716 (t70) cc_final: 0.8332 (t-170) REVERT: A 1088 ILE cc_start: 0.9569 (mm) cc_final: 0.9263 (mm) REVERT: A 1099 MET cc_start: 0.5451 (ptp) cc_final: 0.5037 (tpt) REVERT: A 1190 GLU cc_start: 0.9138 (tp30) cc_final: 0.8930 (tp30) REVERT: A 1232 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8812 (mm-30) REVERT: A 1266 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8493 (t80) REVERT: A 1317 LEU cc_start: 0.8995 (tt) cc_final: 0.8782 (pp) REVERT: A 1384 HIS cc_start: 0.9132 (m90) cc_final: 0.8777 (m90) REVERT: A 1396 MET cc_start: 0.7283 (tpt) cc_final: 0.6722 (mmm) REVERT: A 1425 VAL cc_start: 0.8463 (t) cc_final: 0.8261 (t) REVERT: A 1458 PHE cc_start: 0.8981 (t80) cc_final: 0.8536 (t80) outliers start: 35 outliers final: 25 residues processed: 201 average time/residue: 0.1675 time to fit residues: 48.6509 Evaluate side-chains 201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.086361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.072127 restraints weight = 33447.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.074278 restraints weight = 20341.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075783 restraints weight = 14452.078| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8147 Z= 0.209 Angle : 0.735 17.967 11020 Z= 0.363 Chirality : 0.046 0.292 1254 Planarity : 0.004 0.044 1361 Dihedral : 5.397 74.807 1144 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.42 % Allowed : 21.66 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.65 (0.27), residues: 967 helix: 1.78 (0.20), residues: 618 sheet: -0.86 (0.79), residues: 47 loop : 0.11 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.004 0.001 HIS A 475 PHE 0.050 0.002 PHE A1424 TYR 0.012 0.001 TYR A1265 ARG 0.003 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9177 (mm) cc_final: 0.8801 (tp) REVERT: A 60 GLU cc_start: 0.6759 (tp30) cc_final: 0.6436 (tp30) REVERT: A 94 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 169 PHE cc_start: 0.8232 (m-10) cc_final: 0.7033 (m-80) REVERT: A 352 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 381 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7804 (mmtt) REVERT: A 424 MET cc_start: 0.8786 (tpp) cc_final: 0.8475 (tpp) REVERT: A 594 MET cc_start: 0.8644 (mmt) cc_final: 0.8262 (mmm) REVERT: A 596 LEU cc_start: 0.9097 (tp) cc_final: 0.8794 (tp) REVERT: A 623 TYR cc_start: 0.7936 (t80) cc_final: 0.7639 (t80) REVERT: A 642 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8260 (ttm) REVERT: A 724 TYR cc_start: 0.8960 (m-80) cc_final: 0.8399 (m-80) REVERT: A 728 HIS cc_start: 0.8744 (t70) cc_final: 0.8359 (t-170) REVERT: A 1088 ILE cc_start: 0.9571 (mm) cc_final: 0.9264 (mm) REVERT: A 1099 MET cc_start: 0.5484 (ptp) cc_final: 0.5066 (tpt) REVERT: A 1190 GLU cc_start: 0.9164 (tp30) cc_final: 0.8947 (tp30) REVERT: A 1232 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8808 (mm-30) REVERT: A 1266 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8484 (t80) REVERT: A 1296 MET cc_start: 0.8678 (mmt) cc_final: 0.8040 (mmt) REVERT: A 1317 LEU cc_start: 0.9013 (tt) cc_final: 0.8804 (pp) REVERT: A 1319 ASN cc_start: 0.8965 (m-40) cc_final: 0.8709 (m110) REVERT: A 1384 HIS cc_start: 0.9138 (m90) cc_final: 0.8785 (m90) REVERT: A 1396 MET cc_start: 0.7319 (tpt) cc_final: 0.6757 (mmm) REVERT: A 1458 PHE cc_start: 0.8998 (t80) cc_final: 0.8538 (t80) outliers start: 39 outliers final: 27 residues processed: 201 average time/residue: 0.1648 time to fit residues: 48.2595 Evaluate side-chains 198 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 0.0670 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 0.0170 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.087345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072843 restraints weight = 33673.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.075017 restraints weight = 20579.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.076534 restraints weight = 14657.004| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8147 Z= 0.192 Angle : 0.751 18.865 11020 Z= 0.365 Chirality : 0.048 0.364 1254 Planarity : 0.004 0.045 1361 Dihedral : 5.257 75.126 1144 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.97 % Allowed : 23.13 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.62 (0.27), residues: 967 helix: 1.79 (0.20), residues: 617 sheet: -0.45 (0.95), residues: 37 loop : -0.07 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 726 HIS 0.003 0.001 HIS A1409 PHE 0.052 0.002 PHE A1424 TYR 0.016 0.001 TYR A 408 ARG 0.006 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9169 (mm) cc_final: 0.8784 (tp) REVERT: A 94 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8867 (tt) REVERT: A 169 PHE cc_start: 0.8198 (m-10) cc_final: 0.6979 (m-80) REVERT: A 352 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8933 (pp) REVERT: A 482 LEU cc_start: 0.9433 (pp) cc_final: 0.9200 (tp) REVERT: A 594 MET cc_start: 0.8633 (mmt) cc_final: 0.8248 (mmm) REVERT: A 596 LEU cc_start: 0.9056 (tp) cc_final: 0.8751 (tp) REVERT: A 623 TYR cc_start: 0.7956 (t80) cc_final: 0.7682 (t80) REVERT: A 724 TYR cc_start: 0.9027 (m-80) cc_final: 0.8320 (m-80) REVERT: A 728 HIS cc_start: 0.8809 (t70) cc_final: 0.8445 (t-170) REVERT: A 1088 ILE cc_start: 0.9552 (mm) cc_final: 0.9241 (mm) REVERT: A 1099 MET cc_start: 0.5440 (ptp) cc_final: 0.5229 (tpt) REVERT: A 1232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8822 (mm-30) REVERT: A 1266 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 1317 LEU cc_start: 0.8966 (tt) cc_final: 0.8763 (pp) REVERT: A 1384 HIS cc_start: 0.9191 (m90) cc_final: 0.8846 (m90) REVERT: A 1396 MET cc_start: 0.7311 (tpt) cc_final: 0.6721 (mmm) REVERT: A 1423 TRP cc_start: 0.7539 (t60) cc_final: 0.7320 (t60) REVERT: A 1458 PHE cc_start: 0.8999 (t80) cc_final: 0.8539 (t80) outliers start: 35 outliers final: 27 residues processed: 200 average time/residue: 0.1744 time to fit residues: 49.9384 Evaluate side-chains 195 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 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 361 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.087520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.073309 restraints weight = 32982.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075435 restraints weight = 20267.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.076935 restraints weight = 14472.829| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8147 Z= 0.204 Angle : 0.762 13.420 11020 Z= 0.377 Chirality : 0.049 0.350 1254 Planarity : 0.004 0.046 1361 Dihedral : 5.218 75.259 1144 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.85 % Allowed : 24.15 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.27), residues: 967 helix: 1.76 (0.20), residues: 617 sheet: -0.29 (0.98), residues: 37 loop : -0.11 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 726 HIS 0.003 0.001 HIS A 475 PHE 0.053 0.002 PHE A1424 TYR 0.015 0.001 TYR A 408 ARG 0.005 0.000 ARG A1061 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9154 (mm) cc_final: 0.8778 (tp) REVERT: A 94 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8885 (tt) REVERT: A 103 LYS cc_start: 0.9294 (tppt) cc_final: 0.9093 (tppt) REVERT: A 169 PHE cc_start: 0.8229 (m-10) cc_final: 0.7485 (m-80) REVERT: A 352 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8936 (pp) REVERT: A 482 LEU cc_start: 0.9434 (pp) cc_final: 0.9197 (tp) REVERT: A 594 MET cc_start: 0.8603 (mmt) cc_final: 0.8214 (mmm) REVERT: A 623 TYR cc_start: 0.7864 (t80) cc_final: 0.7521 (t80) REVERT: A 636 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9057 (mm) REVERT: A 724 TYR cc_start: 0.8999 (m-80) cc_final: 0.8313 (m-80) REVERT: A 728 HIS cc_start: 0.8812 (t70) cc_final: 0.8462 (t-170) REVERT: A 1088 ILE cc_start: 0.9553 (mm) cc_final: 0.9249 (mm) REVERT: A 1131 ASP cc_start: 0.7673 (m-30) cc_final: 0.7429 (m-30) REVERT: A 1232 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8813 (mm-30) REVERT: A 1266 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8437 (t80) REVERT: A 1288 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8268 (mmmm) REVERT: A 1317 LEU cc_start: 0.8975 (tt) cc_final: 0.8775 (pp) REVERT: A 1384 HIS cc_start: 0.9136 (m90) cc_final: 0.8770 (m90) REVERT: A 1396 MET cc_start: 0.7313 (tpt) cc_final: 0.6725 (mmm) REVERT: A 1423 TRP cc_start: 0.7569 (t60) cc_final: 0.7325 (t60) REVERT: A 1458 PHE cc_start: 0.8978 (t80) cc_final: 0.8500 (t80) outliers start: 34 outliers final: 26 residues processed: 193 average time/residue: 0.1581 time to fit residues: 44.1318 Evaluate side-chains 195 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1266 PHE Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1441 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 361 ASN ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.087044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072651 restraints weight = 33637.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.074780 restraints weight = 20696.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076256 restraints weight = 14833.410| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8147 Z= 0.202 Angle : 0.759 18.187 11020 Z= 0.376 Chirality : 0.048 0.330 1254 Planarity : 0.004 0.046 1361 Dihedral : 5.203 75.452 1144 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.74 % Allowed : 24.04 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.65 (0.27), residues: 967 helix: 1.81 (0.21), residues: 617 sheet: -0.24 (0.98), residues: 37 loop : -0.10 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 726 HIS 0.003 0.001 HIS A1141 PHE 0.055 0.002 PHE A1424 TYR 0.013 0.001 TYR A1265 ARG 0.004 0.000 ARG A1061 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.83 seconds wall clock time: 48 minutes 10.62 seconds (2890.62 seconds total)