Starting phenix.real_space_refine on Tue Sep 24 10:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/09_2024/6d3r_7793.cif" } resolution = 4.3 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= 0.003 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 27 5.16 5 C 4854 2.51 5 N 1348 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 7548 Classifications: {'peptide': 1127} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 27, 'TRANS': 1099} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1524 Unresolved non-hydrogen angles: 1957 Unresolved non-hydrogen dihedrals: 1274 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 8, 'TYR:plan': 19, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 27, 'PHE:plan': 29, 'GLU:plan': 36, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 834 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.41, per 1000 atoms: 0.71 Number of scatterers: 7610 At special positions: 0 Unit cell: (74.3748, 97.7891, 136.354, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 6 15.00 O 1375 8.00 N 1348 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 2.5 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 71.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 45 through 63 Processing helix chain 'A' and resid 69 through 94 removed outlier: 3.842A pdb=" N CYS A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 117 through 166 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.856A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.035A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 215 Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 268 Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 279 through 322 removed outlier: 3.504A pdb=" N LYS A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.927A pdb=" N THR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 377 removed outlier: 3.588A pdb=" N SER A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 550 through 565 Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 638 through 648 removed outlier: 4.104A pdb=" N PHE A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 860 through 884 removed outlier: 3.614A pdb=" N ILE A 864 " --> pdb=" O HIS A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 918 through 938 removed outlier: 3.889A pdb=" N GLY A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 962 removed outlier: 3.564A pdb=" N HIS A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 973 through 1016 Proline residue: A 992 - end of helix removed outlier: 4.970A pdb=" N PHE A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1045 removed outlier: 4.139A pdb=" N PHE A1020 " --> pdb=" O GLN A1016 " (cutoff:3.500A) Proline residue: A1025 - end of helix Processing helix chain 'A' and resid 1045 through 1065 removed outlier: 4.031A pdb=" N SER A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) Proline residue: A1054 - end of helix Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1074 through 1125 Processing helix chain 'A' and resid 1130 through 1142 Processing helix chain 'A' and resid 1143 through 1169 Processing helix chain 'A' and resid 1251 through 1260 removed outlier: 3.552A pdb=" N LEU A1255 " --> pdb=" O GLY A1251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1256 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1280 through 1287 Processing helix chain 'A' and resid 1302 through 1307 Processing helix chain 'A' and resid 1313 through 1324 Processing helix chain 'A' and resid 1326 through 1333 Processing helix chain 'A' and resid 1335 through 1338 Processing helix chain 'A' and resid 1349 through 1364 Processing helix chain 'A' and resid 1374 through 1377 Processing helix chain 'A' and resid 1379 through 1394 removed outlier: 4.847A pdb=" N VAL A1385 " --> pdb=" O ILE A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1428 through 1439 Processing sheet with id=AA1, first strand: chain 'A' and resid 442 through 449 removed outlier: 7.024A pdb=" N GLN A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 399 " --> pdb=" O GLN A 443 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 445 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 397 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 398 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 480 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 492 removed outlier: 6.775A pdb=" N SER A 490 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 455 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 617 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A 628 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 619 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 502 Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1236 removed outlier: 3.540A pdb=" N LEU A1229 " --> pdb=" O ALA A1219 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A1217 " --> pdb=" O ASN A1231 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A1233 " --> pdb=" O THR A1215 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A1215 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A1235 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR A1213 " --> pdb=" O SER A1235 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A1217 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A1266 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A1219 " --> pdb=" O ASN A1264 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A1264 " --> pdb=" O ALA A1219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1288 through 1291 removed outlier: 6.163A pdb=" N LEU A1369 " --> pdb=" O VAL A1400 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER A1402 " --> pdb=" O LEU A1369 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A1371 " --> pdb=" O SER A1402 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A1242 " --> pdb=" O LEU A1401 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY A1243 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE A1418 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A1245 " --> pdb=" O ILE A1418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1300 through 1301 613 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1652 1.32 - 1.45: 2199 1.45 - 1.57: 3802 1.57 - 1.70: 22 1.70 - 1.83: 51 Bond restraints: 7726 Sorted by residual: bond pdb=" O5' ATP A1502 " pdb=" PA ATP A1502 " ideal model delta sigma weight residual 1.579 1.725 -0.146 1.10e-02 8.26e+03 1.77e+02 bond pdb=" O5' ATP A1501 " pdb=" PA ATP A1501 " ideal model delta sigma weight residual 1.579 1.700 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C1' ATP A1502 " pdb=" N9 ATP A1502 " ideal model delta sigma weight residual 1.459 1.592 -0.133 1.40e-02 5.10e+03 8.97e+01 bond pdb=" C1' ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.459 1.558 -0.099 1.40e-02 5.10e+03 5.03e+01 bond pdb=" C1' ATP A1502 " pdb=" C2' ATP A1502 " ideal model delta sigma weight residual 1.531 1.607 -0.076 1.20e-02 6.94e+03 4.02e+01 ... (remaining 7721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 10265 4.34 - 8.69: 270 8.69 - 13.03: 15 13.03 - 17.38: 3 17.38 - 21.72: 1 Bond angle restraints: 10554 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 124.24 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 121.81 15.02 1.00e+00 1.00e+00 2.26e+02 angle pdb=" PA ATP A1502 " pdb=" O3A ATP A1502 " pdb=" PB ATP A1502 " ideal model delta sigma weight residual 136.83 123.71 13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" C2' ATP A1502 " pdb=" C1' ATP A1502 " pdb=" N9 ATP A1502 " ideal model delta sigma weight residual 114.08 127.10 -13.02 1.53e+00 4.27e-01 7.23e+01 ... (remaining 10549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 4411 16.80 - 33.60: 101 33.60 - 50.39: 30 50.39 - 67.19: 28 67.19 - 83.99: 13 Dihedral angle restraints: 4583 sinusoidal: 1326 harmonic: 3257 Sorted by residual: dihedral pdb=" CA GLY A1129 " pdb=" C GLY A1129 " pdb=" N PRO A1130 " pdb=" CA PRO A1130 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASN A1264 " pdb=" C ASN A1264 " pdb=" N THR A1265 " pdb=" CA THR A1265 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C PHE A1120 " pdb=" N PHE A1120 " pdb=" CA PHE A1120 " pdb=" CB PHE A1120 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 4580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 894 0.093 - 0.185: 333 0.185 - 0.278: 61 0.278 - 0.370: 11 0.370 - 0.463: 3 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA PHE A1120 " pdb=" N PHE A1120 " pdb=" C PHE A1120 " pdb=" CB PHE A1120 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PHE A 317 " pdb=" N PHE A 317 " pdb=" C PHE A 317 " pdb=" CB PHE A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB THR A 466 " pdb=" CA THR A 466 " pdb=" OG1 THR A 466 " pdb=" CG2 THR A 466 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1299 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 968 " 0.089 2.00e-02 2.50e+03 5.50e-02 5.29e+01 pdb=" CG PHE A 968 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE A 968 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 968 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 968 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 968 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 968 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 230 " 0.085 2.00e-02 2.50e+03 5.23e-02 4.79e+01 pdb=" CG PHE A 230 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 230 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 230 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 230 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 230 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 230 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 381 " 0.072 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR A 381 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 381 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 381 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 381 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 381 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 381 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 381 " 0.044 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3205 2.89 - 3.39: 8122 3.39 - 3.89: 11849 3.89 - 4.40: 13723 4.40 - 4.90: 20506 Nonbonded interactions: 57405 Sorted by model distance: nonbonded pdb=" OG SER A 50 " pdb=" OG SER A 159 " model vdw 2.385 3.040 nonbonded pdb=" O TRP A 278 " pdb=" OH TYR A1309 " model vdw 2.441 3.040 nonbonded pdb=" N ASP A 44 " pdb=" OD1 ASP A 44 " model vdw 2.449 3.120 nonbonded pdb=" N ASN A 188 " pdb=" OD1 ASN A 188 " model vdw 2.469 3.120 nonbonded pdb=" N SER A 223 " pdb=" N ALA A 224 " model vdw 2.497 2.560 ... (remaining 57400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.017 0.146 7726 Z= 1.108 Angle : 1.749 21.719 10554 Z= 1.235 Chirality : 0.098 0.463 1302 Planarity : 0.010 0.100 1344 Dihedral : 11.893 83.991 2467 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1119 helix: 0.49 (0.17), residues: 724 sheet: 1.24 (0.58), residues: 60 loop : 0.52 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP A 362 HIS 0.037 0.004 HIS A 200 PHE 0.089 0.008 PHE A 968 TYR 0.072 0.006 TYR A 381 ARG 0.010 0.001 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8867 (mt) cc_final: 0.8376 (mt) REVERT: A 172 VAL cc_start: 0.7894 (m) cc_final: 0.7461 (m) REVERT: A 184 LEU cc_start: 0.9316 (tp) cc_final: 0.9026 (tp) REVERT: A 193 ASP cc_start: 0.8724 (p0) cc_final: 0.8349 (t0) REVERT: A 213 MET cc_start: 0.8496 (ttp) cc_final: 0.8154 (tmm) REVERT: A 245 MET cc_start: 0.9239 (ttm) cc_final: 0.8889 (tpp) REVERT: A 246 MET cc_start: 0.8902 (mmm) cc_final: 0.8594 (tmm) REVERT: A 250 ASP cc_start: 0.8871 (m-30) cc_final: 0.8669 (m-30) REVERT: A 351 VAL cc_start: 0.8989 (t) cc_final: 0.8767 (p) REVERT: A 379 GLU cc_start: 0.8193 (mp0) cc_final: 0.7797 (tp30) REVERT: A 402 TRP cc_start: 0.8814 (m100) cc_final: 0.8455 (m100) REVERT: A 1141 MET cc_start: 0.8502 (ttp) cc_final: 0.8246 (tmm) REVERT: A 1370 LEU cc_start: 0.8681 (mp) cc_final: 0.8403 (tt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1908 time to fit residues: 64.8006 Evaluate side-chains 121 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.0040 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7726 Z= 0.254 Angle : 0.677 8.432 10554 Z= 0.391 Chirality : 0.044 0.205 1302 Planarity : 0.005 0.059 1344 Dihedral : 11.196 74.516 1242 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1119 helix: 1.92 (0.18), residues: 727 sheet: 1.62 (0.58), residues: 70 loop : 0.42 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 278 HIS 0.006 0.002 HIS A 953 PHE 0.023 0.002 PHE A 491 TYR 0.011 0.001 TYR A 564 ARG 0.008 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9191 (tp) cc_final: 0.8888 (tp) REVERT: A 90 TYR cc_start: 0.8693 (t80) cc_final: 0.8340 (t80) REVERT: A 193 ASP cc_start: 0.8734 (p0) cc_final: 0.8158 (t0) REVERT: A 194 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8449 (tp30) REVERT: A 200 HIS cc_start: 0.6560 (p90) cc_final: 0.6338 (p90) REVERT: A 213 MET cc_start: 0.8290 (ttp) cc_final: 0.7968 (ppp) REVERT: A 245 MET cc_start: 0.9311 (ttm) cc_final: 0.9060 (tpp) REVERT: A 246 MET cc_start: 0.8828 (mmm) cc_final: 0.8200 (tmm) REVERT: A 250 ASP cc_start: 0.8870 (m-30) cc_final: 0.8451 (m-30) REVERT: A 290 ARG cc_start: 0.9024 (tpt170) cc_final: 0.8292 (tpt90) REVERT: A 344 CYS cc_start: 0.9166 (m) cc_final: 0.8944 (m) REVERT: A 360 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 370 ASN cc_start: 0.9456 (m-40) cc_final: 0.9188 (m110) REVERT: A 379 GLU cc_start: 0.8222 (mp0) cc_final: 0.8021 (tp30) REVERT: A 489 ILE cc_start: 0.8928 (mp) cc_final: 0.8484 (tp) REVERT: A 572 MET cc_start: 0.8247 (mpp) cc_final: 0.7918 (mpp) REVERT: A 573 ASP cc_start: 0.7794 (t70) cc_final: 0.7387 (t0) REVERT: A 602 ILE cc_start: 0.8757 (mt) cc_final: 0.8539 (mm) REVERT: A 1037 PHE cc_start: 0.8463 (t80) cc_final: 0.8250 (t80) REVERT: A 1105 MET cc_start: 0.8717 (ttm) cc_final: 0.8276 (ttp) REVERT: A 1108 GLU cc_start: 0.8734 (tt0) cc_final: 0.8282 (tt0) REVERT: A 1356 MET cc_start: 0.9209 (mtm) cc_final: 0.8971 (ttp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1857 time to fit residues: 41.5215 Evaluate side-chains 111 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7726 Z= 0.292 Angle : 0.630 7.130 10554 Z= 0.360 Chirality : 0.042 0.189 1302 Planarity : 0.004 0.040 1344 Dihedral : 10.746 70.893 1242 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1119 helix: 1.99 (0.19), residues: 734 sheet: 1.20 (0.55), residues: 70 loop : 0.25 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 362 HIS 0.006 0.002 HIS A 953 PHE 0.033 0.002 PHE A 313 TYR 0.010 0.001 TYR A 276 ARG 0.005 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9266 (tp) cc_final: 0.8988 (tp) REVERT: A 176 ILE cc_start: 0.9010 (mm) cc_final: 0.8794 (tp) REVERT: A 190 ASN cc_start: 0.8553 (p0) cc_final: 0.8304 (p0) REVERT: A 193 ASP cc_start: 0.8903 (p0) cc_final: 0.8164 (t0) REVERT: A 194 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8445 (tp30) REVERT: A 213 MET cc_start: 0.8266 (ttp) cc_final: 0.7758 (tmm) REVERT: A 245 MET cc_start: 0.9337 (ttm) cc_final: 0.8802 (tmm) REVERT: A 246 MET cc_start: 0.8870 (mmm) cc_final: 0.8304 (tmm) REVERT: A 250 ASP cc_start: 0.8927 (m-30) cc_final: 0.8351 (m-30) REVERT: A 290 ARG cc_start: 0.8967 (tpt170) cc_final: 0.8345 (tpt90) REVERT: A 344 CYS cc_start: 0.9145 (m) cc_final: 0.8917 (m) REVERT: A 370 ASN cc_start: 0.9419 (m-40) cc_final: 0.9119 (m110) REVERT: A 572 MET cc_start: 0.8296 (mpp) cc_final: 0.7949 (mpp) REVERT: A 573 ASP cc_start: 0.7955 (t70) cc_final: 0.7511 (t0) REVERT: A 989 ASP cc_start: 0.8831 (t70) cc_final: 0.8583 (t70) REVERT: A 1037 PHE cc_start: 0.8483 (t80) cc_final: 0.8223 (t80) REVERT: A 1041 SER cc_start: 0.8665 (p) cc_final: 0.8425 (p) REVERT: A 1105 MET cc_start: 0.8605 (ttm) cc_final: 0.8404 (ttp) REVERT: A 1141 MET cc_start: 0.9034 (tmm) cc_final: 0.8433 (tmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1566 time to fit residues: 30.6665 Evaluate side-chains 90 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7726 Z= 0.317 Angle : 0.653 8.935 10554 Z= 0.366 Chirality : 0.042 0.192 1302 Planarity : 0.004 0.039 1344 Dihedral : 10.260 88.468 1242 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1119 helix: 1.93 (0.19), residues: 722 sheet: 0.52 (0.56), residues: 60 loop : -0.16 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 362 HIS 0.008 0.002 HIS A1089 PHE 0.014 0.002 PHE A 317 TYR 0.011 0.001 TYR A 305 ARG 0.006 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8745 (p0) cc_final: 0.8473 (p0) REVERT: A 213 MET cc_start: 0.8241 (ttp) cc_final: 0.7704 (tmm) REVERT: A 245 MET cc_start: 0.9236 (ttm) cc_final: 0.9002 (tpp) REVERT: A 246 MET cc_start: 0.8721 (mmm) cc_final: 0.8390 (tmm) REVERT: A 250 ASP cc_start: 0.8898 (m-30) cc_final: 0.8155 (m-30) REVERT: A 344 CYS cc_start: 0.9119 (m) cc_final: 0.8875 (m) REVERT: A 370 ASN cc_start: 0.9419 (m-40) cc_final: 0.9065 (m110) REVERT: A 573 ASP cc_start: 0.8151 (t70) cc_final: 0.7542 (t70) REVERT: A 954 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8785 (tm-30) REVERT: A 989 ASP cc_start: 0.8866 (t70) cc_final: 0.8640 (t70) REVERT: A 1037 PHE cc_start: 0.8524 (t80) cc_final: 0.8204 (t80) REVERT: A 1041 SER cc_start: 0.8549 (p) cc_final: 0.8174 (p) REVERT: A 1105 MET cc_start: 0.8650 (ttm) cc_final: 0.8148 (ttp) REVERT: A 1141 MET cc_start: 0.9025 (tmm) cc_final: 0.8428 (tmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1726 time to fit residues: 30.0011 Evaluate side-chains 90 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7726 Z= 0.172 Angle : 0.560 8.938 10554 Z= 0.308 Chirality : 0.040 0.184 1302 Planarity : 0.003 0.059 1344 Dihedral : 9.772 89.195 1242 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.25), residues: 1119 helix: 2.35 (0.19), residues: 720 sheet: 0.64 (0.58), residues: 60 loop : -0.07 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 362 HIS 0.004 0.001 HIS A 953 PHE 0.012 0.001 PHE A 509 TYR 0.009 0.001 TYR A1077 ARG 0.010 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.9315 (mt) cc_final: 0.9102 (tt) REVERT: A 190 ASN cc_start: 0.8713 (p0) cc_final: 0.8354 (p0) REVERT: A 213 MET cc_start: 0.8171 (ttp) cc_final: 0.7595 (tmm) REVERT: A 282 MET cc_start: 0.8392 (mmt) cc_final: 0.8059 (mmp) REVERT: A 290 ARG cc_start: 0.8877 (tpt170) cc_final: 0.8094 (tpt90) REVERT: A 370 ASN cc_start: 0.9375 (m-40) cc_final: 0.9031 (m110) REVERT: A 395 VAL cc_start: 0.8512 (t) cc_final: 0.8169 (p) REVERT: A 573 ASP cc_start: 0.8129 (t70) cc_final: 0.7527 (t70) REVERT: A 954 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 1037 PHE cc_start: 0.8364 (t80) cc_final: 0.8000 (t80) REVERT: A 1041 SER cc_start: 0.8378 (p) cc_final: 0.8173 (p) REVERT: A 1072 PHE cc_start: 0.8199 (m-80) cc_final: 0.7968 (m-80) REVERT: A 1105 MET cc_start: 0.8530 (ttm) cc_final: 0.8019 (ttp) REVERT: A 1141 MET cc_start: 0.9028 (tmm) cc_final: 0.8455 (tmm) REVERT: A 1142 ASN cc_start: 0.8648 (t0) cc_final: 0.8431 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1592 time to fit residues: 29.7749 Evaluate side-chains 105 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 30.0000 chunk 89 optimal weight: 0.0970 chunk 50 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7726 Z= 0.224 Angle : 0.578 10.379 10554 Z= 0.317 Chirality : 0.041 0.184 1302 Planarity : 0.003 0.031 1344 Dihedral : 9.410 82.625 1242 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1119 helix: 2.36 (0.19), residues: 723 sheet: 0.64 (0.58), residues: 58 loop : -0.14 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS A 953 PHE 0.014 0.002 PHE A 317 TYR 0.021 0.001 TYR A 90 ARG 0.006 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8739 (p0) cc_final: 0.8362 (p0) REVERT: A 213 MET cc_start: 0.8201 (ttp) cc_final: 0.7564 (tmm) REVERT: A 290 ARG cc_start: 0.8865 (tpt170) cc_final: 0.8094 (tpt90) REVERT: A 360 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 370 ASN cc_start: 0.9410 (m-40) cc_final: 0.9021 (m110) REVERT: A 573 ASP cc_start: 0.8189 (t70) cc_final: 0.7585 (t70) REVERT: A 954 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8866 (tm-30) REVERT: A 1037 PHE cc_start: 0.8385 (t80) cc_final: 0.7998 (t80) REVERT: A 1041 SER cc_start: 0.8348 (p) cc_final: 0.8121 (p) REVERT: A 1105 MET cc_start: 0.8543 (ttm) cc_final: 0.8038 (ttp) REVERT: A 1141 MET cc_start: 0.9024 (tmm) cc_final: 0.8501 (tmm) REVERT: A 1142 ASN cc_start: 0.8697 (t0) cc_final: 0.8449 (t0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1625 time to fit residues: 29.3596 Evaluate side-chains 96 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7726 Z= 0.181 Angle : 0.557 8.659 10554 Z= 0.301 Chirality : 0.040 0.178 1302 Planarity : 0.003 0.031 1344 Dihedral : 8.956 74.644 1242 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1119 helix: 2.46 (0.19), residues: 724 sheet: 0.60 (0.59), residues: 58 loop : -0.13 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 200 PHE 0.011 0.001 PHE A 509 TYR 0.018 0.001 TYR A 90 ARG 0.007 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8762 (p0) cc_final: 0.8357 (p0) REVERT: A 213 MET cc_start: 0.8176 (ttp) cc_final: 0.7677 (ppp) REVERT: A 290 ARG cc_start: 0.8815 (tpt170) cc_final: 0.8037 (tpt90) REVERT: A 360 GLN cc_start: 0.9256 (tm-30) cc_final: 0.9020 (tm-30) REVERT: A 370 ASN cc_start: 0.9390 (m-40) cc_final: 0.9009 (m110) REVERT: A 573 ASP cc_start: 0.8196 (t70) cc_final: 0.7578 (t70) REVERT: A 1037 PHE cc_start: 0.8337 (t80) cc_final: 0.7943 (t80) REVERT: A 1041 SER cc_start: 0.8249 (p) cc_final: 0.8037 (p) REVERT: A 1050 GLU cc_start: 0.8735 (pt0) cc_final: 0.8379 (pt0) REVERT: A 1064 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5712 (mptt) REVERT: A 1105 MET cc_start: 0.8485 (ttm) cc_final: 0.7994 (ttp) REVERT: A 1141 MET cc_start: 0.9040 (tmm) cc_final: 0.8531 (tmm) REVERT: A 1142 ASN cc_start: 0.8691 (t0) cc_final: 0.8421 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1621 time to fit residues: 30.3078 Evaluate side-chains 102 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7726 Z= 0.201 Angle : 0.596 14.472 10554 Z= 0.317 Chirality : 0.040 0.256 1302 Planarity : 0.004 0.073 1344 Dihedral : 8.706 70.265 1242 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1119 helix: 2.45 (0.19), residues: 723 sheet: 0.90 (0.63), residues: 51 loop : -0.21 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1093 HIS 0.006 0.001 HIS A 200 PHE 0.012 0.001 PHE A 509 TYR 0.008 0.001 TYR A 305 ARG 0.025 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8771 (p0) cc_final: 0.8354 (p0) REVERT: A 213 MET cc_start: 0.8168 (ttp) cc_final: 0.7639 (ppp) REVERT: A 282 MET cc_start: 0.8336 (mmm) cc_final: 0.7966 (mmt) REVERT: A 290 ARG cc_start: 0.8792 (tpt170) cc_final: 0.8048 (tpt90) REVERT: A 360 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8942 (tm-30) REVERT: A 370 ASN cc_start: 0.9389 (m-40) cc_final: 0.9006 (m110) REVERT: A 573 ASP cc_start: 0.8196 (t70) cc_final: 0.7508 (t70) REVERT: A 1037 PHE cc_start: 0.8350 (t80) cc_final: 0.7936 (t80) REVERT: A 1041 SER cc_start: 0.8252 (p) cc_final: 0.8039 (p) REVERT: A 1050 GLU cc_start: 0.8742 (pt0) cc_final: 0.8371 (pt0) REVERT: A 1105 MET cc_start: 0.8487 (ttm) cc_final: 0.8000 (ttp) REVERT: A 1141 MET cc_start: 0.9086 (tmm) cc_final: 0.8601 (tmm) REVERT: A 1142 ASN cc_start: 0.8730 (t0) cc_final: 0.8422 (t0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1640 time to fit residues: 30.9275 Evaluate side-chains 100 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7726 Z= 0.200 Angle : 0.595 12.142 10554 Z= 0.315 Chirality : 0.041 0.238 1302 Planarity : 0.003 0.030 1344 Dihedral : 8.380 67.407 1242 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1119 helix: 2.44 (0.19), residues: 720 sheet: 0.96 (0.63), residues: 51 loop : -0.24 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.005 0.001 HIS A 200 PHE 0.016 0.002 PHE A1170 TYR 0.009 0.001 TYR A 305 ARG 0.004 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8802 (p0) cc_final: 0.8376 (p0) REVERT: A 213 MET cc_start: 0.8202 (ttp) cc_final: 0.7638 (ppp) REVERT: A 250 ASP cc_start: 0.8254 (m-30) cc_final: 0.8044 (m-30) REVERT: A 282 MET cc_start: 0.8294 (mmm) cc_final: 0.7911 (mmt) REVERT: A 290 ARG cc_start: 0.8774 (tpt170) cc_final: 0.8016 (tpt90) REVERT: A 316 PHE cc_start: 0.8612 (t80) cc_final: 0.8318 (t80) REVERT: A 360 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8947 (tm-30) REVERT: A 370 ASN cc_start: 0.9384 (m-40) cc_final: 0.9001 (m110) REVERT: A 573 ASP cc_start: 0.8216 (t70) cc_final: 0.7564 (t0) REVERT: A 989 ASP cc_start: 0.8769 (t70) cc_final: 0.8567 (t70) REVERT: A 1037 PHE cc_start: 0.8342 (t80) cc_final: 0.7986 (t80) REVERT: A 1041 SER cc_start: 0.8227 (p) cc_final: 0.7969 (p) REVERT: A 1050 GLU cc_start: 0.8758 (pt0) cc_final: 0.8381 (pt0) REVERT: A 1141 MET cc_start: 0.9124 (tmm) cc_final: 0.8649 (tmm) REVERT: A 1142 ASN cc_start: 0.8767 (t0) cc_final: 0.8461 (t0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1574 time to fit residues: 30.1465 Evaluate side-chains 102 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7726 Z= 0.281 Angle : 0.650 12.284 10554 Z= 0.350 Chirality : 0.042 0.230 1302 Planarity : 0.003 0.030 1344 Dihedral : 8.292 66.110 1242 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1119 helix: 2.22 (0.19), residues: 722 sheet: 0.87 (0.63), residues: 51 loop : -0.38 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1093 HIS 0.004 0.001 HIS A 200 PHE 0.030 0.002 PHE A 132 TYR 0.011 0.001 TYR A 162 ARG 0.006 0.001 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8820 (p0) cc_final: 0.8375 (p0) REVERT: A 193 ASP cc_start: 0.8975 (p0) cc_final: 0.8060 (t0) REVERT: A 213 MET cc_start: 0.8252 (ttp) cc_final: 0.7529 (tmm) REVERT: A 282 MET cc_start: 0.8377 (mmm) cc_final: 0.7953 (mmt) REVERT: A 370 ASN cc_start: 0.9393 (m-40) cc_final: 0.9004 (m110) REVERT: A 573 ASP cc_start: 0.8271 (t70) cc_final: 0.7606 (t0) REVERT: A 954 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 1037 PHE cc_start: 0.8390 (t80) cc_final: 0.7989 (t80) REVERT: A 1041 SER cc_start: 0.8295 (p) cc_final: 0.7984 (p) REVERT: A 1105 MET cc_start: 0.8647 (ttm) cc_final: 0.8165 (ttp) REVERT: A 1141 MET cc_start: 0.9129 (tmm) cc_final: 0.8603 (tmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1792 time to fit residues: 33.0374 Evaluate side-chains 96 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079741 restraints weight = 31344.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081758 restraints weight = 16985.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083121 restraints weight = 10761.745| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7726 Z= 0.170 Angle : 0.582 10.418 10554 Z= 0.307 Chirality : 0.040 0.211 1302 Planarity : 0.003 0.030 1344 Dihedral : 7.927 67.045 1242 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.68 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1119 helix: 2.49 (0.19), residues: 719 sheet: 0.78 (0.63), residues: 56 loop : -0.26 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1093 HIS 0.006 0.001 HIS A 200 PHE 0.035 0.002 PHE A1115 TYR 0.009 0.001 TYR A1077 ARG 0.005 0.001 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.06 seconds wall clock time: 30 minutes 40.22 seconds (1840.22 seconds total)