Starting phenix.real_space_refine on Sat Dec 28 07:16:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v12_42878/12_2024/8v12_42878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v12_42878/12_2024/8v12_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_42878/12_2024/8v12_42878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v12_42878/12_2024/8v12_42878.map" model { file = "/net/cci-nas-00/data/ceres_data/8v12_42878/12_2024/8v12_42878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v12_42878/12_2024/8v12_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.31, per 1000 atoms: 0.67 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: 2.32 Conformation dependent library (CDL) restraints added in 873.7 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: 1.06 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: 2.68 Time building geometry restraints manager: 2.60 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: 1.870 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.000 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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 : 0.943 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: 0.1901 time to fit residues: 87.4263 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 : 0.854 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.910 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 18 LEU cc_start: 0.8624 (mt) cc_final: 0.8302 (mp) REVERT: A 38 THR cc_start: 0.7359 (p) cc_final: 0.6966 (m) REVERT: A 169 PHE cc_start: 0.6788 (m-10) cc_final: 0.5593 (m-80) REVERT: A 334 LEU cc_start: 0.7692 (mm) cc_final: 0.7465 (mm) REVERT: A 352 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7667 (pp) REVERT: A 1296 MET cc_start: 0.8388 (mmm) cc_final: 0.8001 (mmm) outliers start: 37 outliers final: 12 residues processed: 247 average time/residue: 0.1746 time to fit residues: 60.5736 Evaluate side-chains 193 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 48 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3862 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= 0.209 Angle : 0.700 12.998 11020 Z= 0.355 Chirality : 0.047 0.259 1254 Planarity : 0.004 0.050 1361 Dihedral : 7.088 74.874 1144 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.74 % Allowed : 17.91 % Favored : 78.34 % 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 (0.26), residues: 967 helix: 1.85 (0.20), residues: 611 sheet: -1.39 (0.83), residues: 42 loop : -0.08 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 726 HIS 0.009 0.001 HIS A 8 PHE 0.040 0.002 PHE A1424 TYR 0.019 0.002 TYR A 75 ARG 0.004 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 233 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.927 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 38 THR cc_start: 0.7266 (p) cc_final: 0.6917 (m) REVERT: A 169 PHE cc_start: 0.6867 (m-10) cc_final: 0.5660 (m-80) REVERT: A 334 LEU cc_start: 0.7497 (mm) cc_final: 0.7264 (mm) REVERT: A 352 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 1218 ASN cc_start: 0.7796 (m-40) cc_final: 0.7537 (m-40) REVERT: A 1281 LYS cc_start: 0.8454 (mttt) cc_final: 0.8247 (mttp) REVERT: A 1296 MET cc_start: 0.8353 (mmm) cc_final: 0.7958 (mmm) outliers start: 33 outliers final: 20 residues processed: 222 average time/residue: 0.1744 time to fit residues: 54.7112 Evaluate side-chains 202 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 657 LEU 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 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 87 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 728 HIS ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4266 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= 0.190 Angle : 0.695 14.500 11020 Z= 0.345 Chirality : 0.045 0.260 1254 Planarity : 0.004 0.047 1361 Dihedral : 6.292 75.001 1144 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.42 % Allowed : 18.03 % 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: 1.59 (0.26), residues: 967 helix: 1.84 (0.20), residues: 606 sheet: -1.08 (1.33), residues: 21 loop : -0.18 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 726 HIS 0.006 0.001 HIS A 728 PHE 0.044 0.002 PHE A1424 TYR 0.013 0.002 TYR A 442 ARG 0.004 0.000 ARG A 108 *********************** 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 237 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.847 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 38 THR cc_start: 0.7178 (p) cc_final: 0.6807 (m) REVERT: A 169 PHE cc_start: 0.6991 (m-10) cc_final: 0.5831 (m-80) REVERT: A 334 LEU cc_start: 0.7465 (mm) cc_final: 0.7203 (mm) REVERT: A 352 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 458 ILE cc_start: 0.7607 (tp) cc_final: 0.6842 (tp) REVERT: A 1296 MET cc_start: 0.8132 (mmm) cc_final: 0.7778 (mmm) outliers start: 39 outliers final: 22 residues processed: 221 average time/residue: 0.1856 time to fit residues: 58.4464 Evaluate side-chains 202 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 471 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 537 LEU 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 1280 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 1408 LEU 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 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 133 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8147 Z= 0.259 Angle : 0.724 15.069 11020 Z= 0.366 Chirality : 0.046 0.250 1254 Planarity : 0.004 0.049 1361 Dihedral : 5.984 74.461 1144 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.54 % Allowed : 19.27 % Favored : 76.19 % 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: 1.46 (0.27), residues: 967 helix: 1.68 (0.20), residues: 614 sheet: -0.77 (0.95), residues: 36 loop : -0.12 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.005 0.001 HIS A 475 PHE 0.044 0.002 PHE A1424 TYR 0.020 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 223 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.005 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 169 PHE cc_start: 0.7088 (m-10) cc_final: 0.5796 (m-80) REVERT: A 334 LEU cc_start: 0.7485 (mm) cc_final: 0.7273 (mm) REVERT: A 352 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7695 (pp) REVERT: A 458 ILE cc_start: 0.7796 (tp) cc_final: 0.7519 (tp) outliers start: 40 outliers final: 24 residues processed: 206 average time/residue: 0.1818 time to fit residues: 52.7653 Evaluate side-chains 191 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 321 LEU 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 512 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 569 VAL 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 1280 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 1408 LEU 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 31 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4831 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= 0.202 Angle : 0.748 15.932 11020 Z= 0.367 Chirality : 0.047 0.301 1254 Planarity : 0.004 0.049 1361 Dihedral : 5.748 74.379 1144 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.63 % Allowed : 21.66 % Favored : 74.72 % 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: 1.37 (0.26), residues: 967 helix: 1.58 (0.20), residues: 617 sheet: -1.29 (1.12), residues: 27 loop : -0.10 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 726 HIS 0.005 0.001 HIS A 475 PHE 0.042 0.002 PHE A1380 TYR 0.017 0.002 TYR A 408 ARG 0.008 0.000 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 217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 PHE cc_start: 0.7090 (m-10) cc_final: 0.5893 (m-80) REVERT: A 352 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 1194 MET cc_start: 0.7352 (ttp) cc_final: 0.7080 (ttp) REVERT: A 1410 LEU cc_start: 0.8780 (tt) cc_final: 0.8520 (tt) outliers start: 32 outliers final: 20 residues processed: 204 average time/residue: 0.1780 time to fit residues: 52.1229 Evaluate side-chains 191 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 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 647 LEU Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1149 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8147 Z= 0.222 Angle : 0.769 18.034 11020 Z= 0.378 Chirality : 0.047 0.380 1254 Planarity : 0.004 0.054 1361 Dihedral : 5.568 74.441 1144 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.51 % Allowed : 22.56 % 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: 1.36 (0.27), residues: 967 helix: 1.57 (0.20), residues: 617 sheet: -0.82 (0.86), residues: 42 loop : -0.10 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 726 HIS 0.005 0.001 HIS A 475 PHE 0.044 0.002 PHE A1380 TYR 0.038 0.002 TYR A 304 ARG 0.007 0.001 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 214 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7945 (tppt) cc_final: 0.7156 (tppt) REVERT: A 169 PHE cc_start: 0.7226 (m-10) cc_final: 0.5935 (m-80) REVERT: A 352 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7762 (pp) outliers start: 31 outliers final: 20 residues processed: 203 average time/residue: 0.1643 time to fit residues: 47.6846 Evaluate side-chains 189 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 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 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 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 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** A1228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8147 Z= 0.205 Angle : 0.805 18.941 11020 Z= 0.397 Chirality : 0.049 0.321 1254 Planarity : 0.004 0.052 1361 Dihedral : 5.515 74.717 1144 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.40 % Allowed : 23.02 % Favored : 73.58 % 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: 1.30 (0.27), residues: 967 helix: 1.51 (0.20), residues: 610 sheet: -0.73 (0.80), residues: 47 loop : -0.06 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.005 0.001 HIS A 475 PHE 0.044 0.002 PHE A1424 TYR 0.030 0.002 TYR A 304 ARG 0.005 0.000 ARG A 90 *********************** 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 215 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 PHE cc_start: 0.7196 (m-10) cc_final: 0.5969 (m-80) REVERT: A 352 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7704 (pp) outliers start: 30 outliers final: 21 residues processed: 200 average time/residue: 0.1677 time to fit residues: 48.9041 Evaluate side-chains 194 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 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 599 SER Chi-restraints excluded: chain A residue 643 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8147 Z= 0.208 Angle : 0.813 18.818 11020 Z= 0.397 Chirality : 0.049 0.338 1254 Planarity : 0.004 0.056 1361 Dihedral : 5.348 75.049 1144 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.40 % Allowed : 24.38 % 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: 1.36 (0.27), residues: 967 helix: 1.56 (0.20), residues: 610 sheet: -0.12 (0.99), residues: 36 loop : -0.13 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.007 0.001 HIS A 475 PHE 0.045 0.002 PHE A1424 TYR 0.035 0.002 TYR A 623 ARG 0.004 0.000 ARG A 90 *********************** 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 209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 PHE cc_start: 0.7204 (m-10) cc_final: 0.5906 (m-80) REVERT: A 352 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 1423 TRP cc_start: 0.6328 (t60) cc_final: 0.5928 (t60) outliers start: 30 outliers final: 25 residues processed: 198 average time/residue: 0.1585 time to fit residues: 45.5030 Evaluate side-chains 201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 471 PHE Chi-restraints excluded: chain A residue 501 LEU 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 629 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5694 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= 0.214 Angle : 0.848 13.796 11020 Z= 0.420 Chirality : 0.050 0.355 1254 Planarity : 0.004 0.047 1361 Dihedral : 5.307 75.407 1144 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.17 % Allowed : 24.94 % Favored : 71.88 % Cbeta Deviations : 0.11 % 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: 1.28 (0.26), residues: 967 helix: 1.52 (0.20), residues: 610 sheet: -0.90 (1.17), residues: 26 loop : -0.17 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 726 HIS 0.014 0.002 HIS A1264 PHE 0.048 0.002 PHE A1424 TYR 0.026 0.002 TYR A 304 ARG 0.003 0.000 ARG A 335 ********************** 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 206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 PHE cc_start: 0.7195 (m-10) cc_final: 0.5912 (m-80) REVERT: A 352 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 482 LEU cc_start: 0.8833 (pp) cc_final: 0.8585 (tp) REVERT: A 540 LEU cc_start: 0.8398 (mt) cc_final: 0.8079 (mt) REVERT: A 1423 TRP cc_start: 0.6203 (t60) cc_final: 0.5853 (t60) outliers start: 28 outliers final: 24 residues processed: 196 average time/residue: 0.1903 time to fit residues: 53.4814 Evaluate side-chains 196 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 471 PHE Chi-restraints excluded: chain A residue 501 LEU 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 629 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 VAL 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 1304 ILE Chi-restraints excluded: chain A residue 1374 LEU 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 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.087884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.073942 restraints weight = 32853.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.076049 restraints weight = 20210.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.077532 restraints weight = 14383.660| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5886 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= 0.211 Angle : 0.877 25.172 11020 Z= 0.430 Chirality : 0.050 0.350 1254 Planarity : 0.004 0.047 1361 Dihedral : 5.226 75.804 1144 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.17 % Allowed : 26.08 % Favored : 70.75 % 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: 1.28 (0.27), residues: 967 helix: 1.53 (0.21), residues: 610 sheet: -0.83 (1.18), residues: 26 loop : -0.19 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 726 HIS 0.005 0.001 HIS A 475 PHE 0.051 0.002 PHE A1424 TYR 0.026 0.001 TYR A 408 ARG 0.003 0.000 ARG A 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.17 seconds wall clock time: 36 minutes 49.92 seconds (2209.92 seconds total)