Starting phenix.real_space_refine (version: dev) on Sun Feb 19 18:28:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2023/7q5z_13847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2023/7q5z_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_2023/7q5z_13847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2023/7q5z_13847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2023/7q5z_13847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5z_13847/02_2023/7q5z_13847.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.22, per 1000 atoms: 0.59 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: 3.84 Conformation dependent library (CDL) restraints added in 1.5 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: 1.27 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: 4.76 Time building geometry restraints manager: 4.26 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 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. 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: 1.650 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: 6.320 Check model and map are aligned: 0.180 Process input model: 31.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 % 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 *********************** 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 : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.1913 time to fit residues: 34.7473 Evaluate side-chains 84 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1056 time to fit residues: 1.8965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7001 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 0.059 10723 Z= 0.177 Angle : 0.597 11.261 14571 Z= 0.303 Chirality : 0.044 0.150 1659 Planarity : 0.005 0.085 1870 Dihedral : 4.831 25.975 1435 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.33 % Favored : 94.44 % Rotamer Outliers : 0.85 % 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: -1.54 (0.22), residues: 1332 helix: -1.22 (0.31), residues: 210 sheet: 0.12 (0.23), residues: 535 loop : -2.04 (0.23), residues: 587 *********************** 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 108 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 0.1957 time to fit residues: 31.1896 Evaluate side-chains 91 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1149 time to fit residues: 3.5114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10723 Z= 0.156 Angle : 0.559 7.935 14571 Z= 0.283 Chirality : 0.044 0.157 1659 Planarity : 0.004 0.065 1870 Dihedral : 4.495 23.877 1435 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer Outliers : 0.85 % 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: -1.13 (0.23), residues: 1332 helix: -0.35 (0.34), residues: 212 sheet: 0.29 (0.23), residues: 523 loop : -1.88 (0.24), residues: 597 *********************** 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 107 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.2005 time to fit residues: 32.6262 Evaluate side-chains 91 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1092 time to fit residues: 2.6243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 0.0570 chunk 58 optimal weight: 0.0050 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 10723 Z= 0.156 Angle : 0.556 12.902 14571 Z= 0.279 Chirality : 0.043 0.149 1659 Planarity : 0.004 0.055 1870 Dihedral : 4.368 24.328 1435 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.33 % Favored : 94.52 % Rotamer Outliers : 0.85 % 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: -0.97 (0.23), residues: 1332 helix: 0.04 (0.35), residues: 212 sheet: 0.32 (0.23), residues: 524 loop : -1.80 (0.24), residues: 596 *********************** 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 103 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.187 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.1975 time to fit residues: 30.4101 Evaluate side-chains 90 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1425 time to fit residues: 3.4951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 854 HIS ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 10723 Z= 0.249 Angle : 0.604 12.522 14571 Z= 0.303 Chirality : 0.044 0.150 1659 Planarity : 0.004 0.050 1870 Dihedral : 4.469 24.898 1435 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer Outliers : 1.11 % 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: -0.96 (0.23), residues: 1332 helix: -0.03 (0.35), residues: 211 sheet: 0.32 (0.24), residues: 515 loop : -1.74 (0.24), residues: 606 *********************** 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 103 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.1842 time to fit residues: 29.6166 Evaluate side-chains 87 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1098 time to fit residues: 3.0626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 10723 Z= 0.210 Angle : 0.583 10.661 14571 Z= 0.292 Chirality : 0.044 0.150 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.435 24.710 1435 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer Outliers : 1.11 % 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: 0.24 (0.36), residues: 211 sheet: 0.33 (0.24), residues: 515 loop : -1.71 (0.25), residues: 606 *********************** 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 96 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.245 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 92 average time/residue: 0.2035 time to fit residues: 30.1612 Evaluate side-chains 86 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1577 time to fit residues: 3.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 166 ASN A 857 ASN ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 HIS ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.129 10723 Z= 0.332 Angle : 0.649 10.915 14571 Z= 0.330 Chirality : 0.046 0.157 1659 Planarity : 0.004 0.051 1870 Dihedral : 4.746 26.923 1435 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.87 % Rotamer Outliers : 1.45 % 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: -0.23 (0.34), residues: 213 sheet: 0.27 (0.23), residues: 513 loop : -1.69 (0.25), residues: 606 *********************** 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 98 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.189 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.1973 time to fit residues: 28.4940 Evaluate side-chains 85 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1253 time to fit residues: 4.5882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7108 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 10723 Z= 0.211 Angle : 0.614 18.239 14571 Z= 0.305 Chirality : 0.044 0.213 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.541 25.314 1435 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.22 % Rotamer Outliers : 0.51 % 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: 0.22 (0.36), residues: 212 sheet: 0.25 (0.23), residues: 518 loop : -1.62 (0.25), residues: 602 *********************** 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 90 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.354 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.1826 time to fit residues: 25.6495 Evaluate side-chains 85 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1130 time to fit residues: 2.8627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7083 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 10723 Z= 0.187 Angle : 0.606 17.172 14571 Z= 0.300 Chirality : 0.044 0.182 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.421 25.616 1435 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.77 % Rotamer Outliers : 0.34 % 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: -0.76 (0.24), residues: 1332 helix: 0.36 (0.36), residues: 213 sheet: 0.34 (0.24), residues: 513 loop : -1.58 (0.25), residues: 606 *********************** 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 86 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.263 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1801 time to fit residues: 25.1057 Evaluate side-chains 82 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1082 time to fit residues: 2.3343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 122 optimal weight: 0.0050 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7071 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 10723 Z= 0.183 Angle : 0.598 16.996 14571 Z= 0.295 Chirality : 0.044 0.217 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.324 24.938 1435 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.07 % Rotamer Outliers : 0.17 % 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: -0.68 (0.24), residues: 1332 helix: 0.43 (0.36), residues: 212 sheet: 0.41 (0.24), residues: 513 loop : -1.55 (0.25), residues: 607 ********************** 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 81 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.1853 time to fit residues: 24.8032 Evaluate side-chains 76 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1094 time to fit residues: 1.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.150411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.116190 restraints weight = 25813.346| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 4.11 r_work: 0.3809 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.109 10723 Z= 0.281 Angle : 0.654 17.219 14571 Z= 0.323 Chirality : 0.045 0.257 1659 Planarity : 0.004 0.044 1870 Dihedral : 4.495 26.407 1435 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.38 % Favored : 93.39 % Rotamer Outliers : 0.34 % 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: 0.07 (0.35), residues: 211 sheet: 0.37 (0.24), residues: 513 loop : -1.55 (0.25), residues: 608 =============================================================================== Job complete usr+sys time: 2191.60 seconds wall clock time: 41 minutes 9.62 seconds (2469.62 seconds total)