Starting phenix.real_space_refine on Wed Feb 14 23:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2024/7q5z_13847.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 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 52 5.16 5 C 6709 2.51 5 N 1719 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A ASP 1113": "OD1" <-> "OD2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1332": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10489 Classifications: {'peptide': 1344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 70, 'TRANS': 1272} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.34, per 1000 atoms: 0.51 Number of scatterers: 10489 At special positions: 0 Unit cell: (87.2329, 106.004, 141.339, 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 52 16.00 O 2009 8.00 N 1719 7.00 C 6709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1453 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 16.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 365 through 369 removed outlier: 4.164A pdb=" N ASP A 368 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 4.100A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 973 through 977 removed outlier: 3.755A pdb=" N VAL A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 991 removed outlier: 3.652A pdb=" N ILE A 982 " --> pdb=" O PHE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1014 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1055 through 1069 removed outlier: 3.900A pdb=" N ILE A1059 " --> pdb=" O ASP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1109 removed outlier: 3.531A pdb=" N GLY A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1133 through 1147 removed outlier: 3.737A pdb=" N ALA A1147 " --> pdb=" O ILE A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 3.997A pdb=" N ILE A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 removed outlier: 3.689A pdb=" N GLU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.602A pdb=" N LYS A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1255 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.962A pdb=" N ARG A1283 " --> pdb=" O SER A1280 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1284 " --> pdb=" O VAL A1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1284' Processing helix chain 'A' and resid 1380 through 1387 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 56 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.487A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 285 removed outlier: 6.517A pdb=" N ALA A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A 317 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN A 255 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 315 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 257 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A 313 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS A 259 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 311 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS A 261 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.513A pdb=" N VAL A 470 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AB3, first strand: chain 'A' and resid 499 through 501 removed outlier: 5.792A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB5, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB6, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 removed outlier: 3.644A pdb=" N THR A 811 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 795 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 809 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 832 through 836 Processing sheet with id=AB9, first strand: chain 'A' and resid 799 through 801 removed outlier: 6.269A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC2, first strand: chain 'A' and resid 908 through 913 removed outlier: 3.880A pdb=" N TYR A1309 " --> pdb=" O LEU A 949 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 921 through 930 removed outlier: 4.485A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1164 through 1167 Processing sheet with id=AC5, first strand: chain 'A' and resid 1327 through 1332 Processing sheet with id=AC6, first strand: chain 'A' and resid 1393 through 1396 removed outlier: 4.014A pdb=" N LYS A1393 " --> pdb=" O TYR A1404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A1432 " --> pdb=" O LYS A1370 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1134 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: 4.74 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3209 1.34 - 1.46: 2476 1.46 - 1.58: 4958 1.58 - 1.71: 1 1.71 - 1.83: 79 Bond restraints: 10723 Sorted by residual: bond pdb=" CA ASP A1113 " pdb=" C ASP A1113 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.41e-02 5.03e+03 7.95e+00 bond pdb=" N ASP A 367 " pdb=" CA ASP A 367 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" C SER A1343 " pdb=" N PRO A1344 " ideal model delta sigma weight residual 1.334 1.386 -0.053 2.34e-02 1.83e+03 5.04e+00 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA MET A1378 " pdb=" CB MET A1378 " ideal model delta sigma weight residual 1.513 1.561 -0.048 2.59e-02 1.49e+03 3.38e+00 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.08: 230 105.08 - 112.32: 5232 112.32 - 119.56: 3687 119.56 - 126.80: 5266 126.80 - 134.03: 156 Bond angle restraints: 14571 Sorted by residual: angle pdb=" N ILE A 760 " pdb=" CA ILE A 760 " pdb=" C ILE A 760 " ideal model delta sigma weight residual 113.47 106.82 6.65 1.01e+00 9.80e-01 4.34e+01 angle pdb=" CB MET A1087 " pdb=" CG MET A1087 " pdb=" SD MET A1087 " ideal model delta sigma weight residual 112.70 130.90 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" N GLU A1007 " pdb=" CA GLU A1007 " pdb=" CB GLU A1007 " ideal model delta sigma weight residual 110.40 119.96 -9.56 1.63e+00 3.76e-01 3.44e+01 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.73e+01 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5952 17.63 - 35.25: 416 35.25 - 52.88: 68 52.88 - 70.51: 15 70.51 - 88.13: 8 Dihedral angle restraints: 6459 sinusoidal: 2552 harmonic: 3907 Sorted by residual: dihedral pdb=" CA PHE A1235 " pdb=" C PHE A1235 " pdb=" N SER A1236 " pdb=" CA SER A1236 " ideal model delta harmonic sigma weight residual 180.00 -148.90 -31.10 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ALA A1086 " pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LYS A1088 " pdb=" C LYS A1088 " pdb=" N GLY A1089 " pdb=" CA GLY A1089 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 6456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1517 0.109 - 0.217: 133 0.217 - 0.326: 6 0.326 - 0.435: 1 0.435 - 0.544: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB VAL A 594 " pdb=" CA VAL A 594 " pdb=" CG1 VAL A 594 " pdb=" CG2 VAL A 594 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1656 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 84 " -0.102 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO A 85 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " 0.040 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR A1142 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1113 " 0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" CG ASP A1113 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASP A1113 " 0.028 2.00e-02 2.50e+03 pdb=" OD2 ASP A1113 " 0.026 2.00e-02 2.50e+03 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 9 2.38 - 3.01: 5119 3.01 - 3.64: 15503 3.64 - 4.27: 23295 4.27 - 4.90: 39032 Nonbonded interactions: 82958 Sorted by model distance: nonbonded pdb=" SG CYS A 970 " pdb=" CD GLN A 973 " model vdw 1.750 3.630 nonbonded pdb=" O THR A1038 " pdb=" OG1 THR A1042 " model vdw 2.323 2.440 nonbonded pdb=" OG1 THR A 58 " pdb=" O LYS A 61 " model vdw 2.337 2.440 nonbonded pdb=" OE1 GLU A 972 " pdb=" OH TYR A1439 " model vdw 2.352 2.440 nonbonded pdb=" O PRO A1377 " pdb=" OG1 THR A1381 " model vdw 2.359 2.440 ... (remaining 82953 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.450 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.880 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.005 0.100 10723 Z= 0.307 Angle : 1.003 18.201 14571 Z= 0.517 Chirality : 0.062 0.544 1659 Planarity : 0.008 0.151 1870 Dihedral : 12.761 88.132 3916 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.62 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.21), residues: 1332 helix: -2.57 (0.26), residues: 211 sheet: 0.06 (0.23), residues: 526 loop : -2.25 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1224 HIS 0.002 0.001 HIS A1084 PHE 0.028 0.003 PHE A1040 TYR 0.100 0.003 TYR A1142 ARG 0.004 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 PHE cc_start: 0.8053 (p90) cc_final: 0.7606 (p90) REVERT: A 523 THR cc_start: 0.7805 (p) cc_final: 0.7490 (p) REVERT: A 531 ASP cc_start: 0.8375 (p0) cc_final: 0.7609 (p0) REVERT: A 988 LEU cc_start: 0.8280 (mt) cc_final: 0.7799 (mt) REVERT: A 1060 GLN cc_start: 0.6778 (tm-30) cc_final: 0.6452 (tm-30) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.1847 time to fit residues: 33.7162 Evaluate side-chains 86 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10723 Z= 0.174 Angle : 0.593 11.583 14571 Z= 0.300 Chirality : 0.044 0.156 1659 Planarity : 0.005 0.086 1870 Dihedral : 5.005 50.227 1438 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.48 % Favored : 94.29 % Rotamer: Outliers : 0.77 % Allowed : 6.91 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.53 (0.22), residues: 1332 helix: -1.20 (0.31), residues: 211 sheet: 0.13 (0.23), residues: 535 loop : -2.03 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1224 HIS 0.003 0.001 HIS A1084 PHE 0.017 0.001 PHE A 219 TYR 0.026 0.001 TYR A1142 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8390 (p0) cc_final: 0.7582 (p0) REVERT: A 1037 LEU cc_start: 0.7979 (tp) cc_final: 0.7654 (tp) REVERT: A 1060 GLN cc_start: 0.6800 (tm-30) cc_final: 0.6412 (tm-30) outliers start: 9 outliers final: 8 residues processed: 101 average time/residue: 0.2020 time to fit residues: 31.5914 Evaluate side-chains 93 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0670 chunk 37 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 HIS ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10723 Z= 0.169 Angle : 0.562 8.087 14571 Z= 0.286 Chirality : 0.044 0.158 1659 Planarity : 0.004 0.065 1870 Dihedral : 4.547 24.356 1435 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.28 % Allowed : 8.78 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.18 (0.23), residues: 1332 helix: -0.45 (0.34), residues: 212 sheet: 0.32 (0.23), residues: 518 loop : -1.92 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1224 HIS 0.003 0.000 HIS A1084 PHE 0.012 0.001 PHE A 618 TYR 0.014 0.001 TYR A 537 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 99 SER cc_start: 0.7154 (p) cc_final: 0.6854 (m) REVERT: A 531 ASP cc_start: 0.8393 (p0) cc_final: 0.7578 (p0) REVERT: A 1037 LEU cc_start: 0.7929 (tp) cc_final: 0.7616 (tp) REVERT: A 1060 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6380 (tm-30) REVERT: A 1206 THR cc_start: 0.6403 (OUTLIER) cc_final: 0.5321 (m) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.1799 time to fit residues: 28.8807 Evaluate side-chains 99 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10723 Z= 0.166 Angle : 0.558 12.447 14571 Z= 0.282 Chirality : 0.043 0.151 1659 Planarity : 0.004 0.055 1870 Dihedral : 4.389 24.007 1435 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 1.62 % Allowed : 10.32 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.02 (0.23), residues: 1332 helix: -0.14 (0.35), residues: 212 sheet: 0.35 (0.24), residues: 514 loop : -1.81 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 PHE 0.011 0.001 PHE A 618 TYR 0.013 0.001 TYR A 620 ARG 0.001 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8247 (m-40) cc_final: 0.7913 (m-40) REVERT: A 56 LEU cc_start: 0.8377 (pt) cc_final: 0.7662 (tp) REVERT: A 192 MET cc_start: 0.6957 (mpp) cc_final: 0.6636 (mmp) REVERT: A 492 TYR cc_start: 0.7685 (m-80) cc_final: 0.7477 (m-80) REVERT: A 531 ASP cc_start: 0.8393 (p0) cc_final: 0.7584 (p0) REVERT: A 1037 LEU cc_start: 0.7934 (tp) cc_final: 0.7624 (tp) REVERT: A 1060 GLN cc_start: 0.6753 (tm-30) cc_final: 0.6340 (tm-30) REVERT: A 1206 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.5415 (m) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.1837 time to fit residues: 29.9965 Evaluate side-chains 102 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10723 Z= 0.186 Angle : 0.565 12.201 14571 Z= 0.282 Chirality : 0.044 0.149 1659 Planarity : 0.004 0.050 1870 Dihedral : 4.368 24.216 1435 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 1.79 % Allowed : 11.34 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.87 (0.23), residues: 1332 helix: 0.12 (0.35), residues: 212 sheet: 0.40 (0.24), residues: 509 loop : -1.71 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.012 0.001 PHE A1053 TYR 0.013 0.001 TYR A1436 ARG 0.001 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8275 (m-40) cc_final: 0.7900 (m-40) REVERT: A 192 MET cc_start: 0.6906 (mpp) cc_final: 0.6639 (mmp) REVERT: A 492 TYR cc_start: 0.7662 (m-80) cc_final: 0.7275 (m-80) REVERT: A 531 ASP cc_start: 0.8454 (p0) cc_final: 0.7835 (p0) REVERT: A 1037 LEU cc_start: 0.7931 (tp) cc_final: 0.7497 (tp) REVERT: A 1060 GLN cc_start: 0.6773 (tm-30) cc_final: 0.6341 (tm-30) REVERT: A 1206 THR cc_start: 0.6043 (OUTLIER) cc_final: 0.5068 (m) REVERT: A 1378 MET cc_start: 0.7562 (tmm) cc_final: 0.7296 (tmm) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.1785 time to fit residues: 30.5005 Evaluate side-chains 105 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 76 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10723 Z= 0.238 Angle : 0.589 11.223 14571 Z= 0.298 Chirality : 0.044 0.156 1659 Planarity : 0.004 0.047 1870 Dihedral : 4.456 25.264 1435 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.39 % Allowed : 12.70 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.87 (0.23), residues: 1332 helix: 0.10 (0.35), residues: 211 sheet: 0.31 (0.24), residues: 516 loop : -1.63 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 837 HIS 0.005 0.001 HIS A1084 PHE 0.014 0.001 PHE A1053 TYR 0.030 0.001 TYR A1142 ARG 0.002 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 192 MET cc_start: 0.6999 (mpp) cc_final: 0.6722 (mmt) REVERT: A 492 TYR cc_start: 0.7773 (m-80) cc_final: 0.7331 (m-80) REVERT: A 531 ASP cc_start: 0.8507 (p0) cc_final: 0.7838 (p0) REVERT: A 1060 GLN cc_start: 0.6895 (tm-30) cc_final: 0.6439 (tm-30) REVERT: A 1206 THR cc_start: 0.6196 (OUTLIER) cc_final: 0.5209 (m) outliers start: 28 outliers final: 19 residues processed: 109 average time/residue: 0.1768 time to fit residues: 30.8684 Evaluate side-chains 105 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 ASN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 10723 Z= 0.296 Angle : 0.624 11.748 14571 Z= 0.314 Chirality : 0.045 0.164 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.617 26.036 1435 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 2.22 % Allowed : 13.98 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.95 (0.23), residues: 1332 helix: -0.09 (0.35), residues: 212 sheet: 0.27 (0.24), residues: 519 loop : -1.65 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 837 HIS 0.005 0.001 HIS A1084 PHE 0.015 0.002 PHE A1053 TYR 0.018 0.002 TYR A1436 ARG 0.002 0.000 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 99 SER cc_start: 0.7246 (p) cc_final: 0.6963 (m) REVERT: A 492 TYR cc_start: 0.7891 (m-80) cc_final: 0.7409 (m-80) REVERT: A 531 ASP cc_start: 0.8556 (p0) cc_final: 0.7888 (p0) REVERT: A 1116 MET cc_start: 0.7181 (mmp) cc_final: 0.6839 (mmp) REVERT: A 1206 THR cc_start: 0.5696 (OUTLIER) cc_final: 0.4984 (m) outliers start: 26 outliers final: 20 residues processed: 104 average time/residue: 0.1833 time to fit residues: 31.4499 Evaluate side-chains 104 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10723 Z= 0.196 Angle : 0.609 18.504 14571 Z= 0.299 Chirality : 0.044 0.157 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.483 25.317 1435 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.93 % Favored : 93.84 % Rotamer: Outliers : 2.22 % Allowed : 13.64 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.80 (0.23), residues: 1332 helix: 0.23 (0.35), residues: 213 sheet: 0.32 (0.24), residues: 519 loop : -1.59 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 837 HIS 0.003 0.000 HIS A 914 PHE 0.012 0.001 PHE A 618 TYR 0.016 0.001 TYR A 732 ARG 0.001 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8306 (m-40) cc_final: 0.7889 (m-40) REVERT: A 99 SER cc_start: 0.7305 (p) cc_final: 0.7082 (m) REVERT: A 192 MET cc_start: 0.6449 (mmt) cc_final: 0.6187 (mpp) REVERT: A 342 MET cc_start: 0.1601 (mmm) cc_final: 0.1292 (mmm) REVERT: A 492 TYR cc_start: 0.7905 (m-80) cc_final: 0.7461 (m-80) REVERT: A 531 ASP cc_start: 0.8427 (p0) cc_final: 0.7765 (p0) REVERT: A 1037 LEU cc_start: 0.7875 (tp) cc_final: 0.7566 (tp) REVERT: A 1116 MET cc_start: 0.7160 (mmp) cc_final: 0.6924 (mmp) REVERT: A 1206 THR cc_start: 0.6120 (OUTLIER) cc_final: 0.5273 (m) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.1983 time to fit residues: 33.3366 Evaluate side-chains 107 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10723 Z= 0.203 Angle : 0.601 17.332 14571 Z= 0.297 Chirality : 0.044 0.156 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.433 25.479 1435 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.07 % Rotamer: Outliers : 2.30 % Allowed : 13.64 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.73 (0.23), residues: 1332 helix: 0.36 (0.36), residues: 212 sheet: 0.31 (0.23), residues: 523 loop : -1.53 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 PHE 0.012 0.001 PHE A 618 TYR 0.046 0.001 TYR A1142 ARG 0.001 0.000 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8320 (m-40) cc_final: 0.7884 (m-40) REVERT: A 192 MET cc_start: 0.6492 (mmt) cc_final: 0.6216 (mpp) REVERT: A 342 MET cc_start: 0.1819 (mmm) cc_final: 0.1489 (mmm) REVERT: A 492 TYR cc_start: 0.7915 (m-80) cc_final: 0.7553 (m-80) REVERT: A 531 ASP cc_start: 0.8427 (p0) cc_final: 0.7763 (p0) REVERT: A 1037 LEU cc_start: 0.7837 (tp) cc_final: 0.7519 (tp) REVERT: A 1206 THR cc_start: 0.6084 (OUTLIER) cc_final: 0.5212 (m) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.1733 time to fit residues: 29.8708 Evaluate side-chains 111 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 10723 Z= 0.245 Angle : 0.625 17.425 14571 Z= 0.309 Chirality : 0.045 0.202 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.509 25.802 1435 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 2.39 % Allowed : 13.55 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.79 (0.23), residues: 1332 helix: 0.19 (0.35), residues: 211 sheet: 0.28 (0.24), residues: 524 loop : -1.51 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.014 0.001 PHE A 618 TYR 0.065 0.002 TYR A1142 ARG 0.002 0.000 ARG A 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 192 MET cc_start: 0.6553 (mmt) cc_final: 0.6256 (mpp) REVERT: A 492 TYR cc_start: 0.7952 (m-80) cc_final: 0.7635 (m-80) REVERT: A 531 ASP cc_start: 0.8453 (p0) cc_final: 0.7777 (p0) REVERT: A 1037 LEU cc_start: 0.7960 (tp) cc_final: 0.7758 (tp) REVERT: A 1116 MET cc_start: 0.7260 (mmp) cc_final: 0.7038 (mmp) REVERT: A 1206 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5032 (m) outliers start: 28 outliers final: 23 residues processed: 104 average time/residue: 0.1669 time to fit residues: 28.1513 Evaluate side-chains 108 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.149654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.115502 restraints weight = 25707.950| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.08 r_work: 0.3796 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10723 Z= 0.265 Angle : 0.636 17.419 14571 Z= 0.317 Chirality : 0.045 0.217 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.608 26.506 1435 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 2.22 % Allowed : 13.64 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.81 (0.23), residues: 1332 helix: 0.07 (0.35), residues: 212 sheet: 0.27 (0.24), residues: 523 loop : -1.49 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 837 HIS 0.005 0.001 HIS A1084 PHE 0.015 0.002 PHE A 618 TYR 0.074 0.002 TYR A1142 ARG 0.002 0.000 ARG A 807 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.10 seconds wall clock time: 44 minutes 20.61 seconds (2660.61 seconds total)