Starting phenix.real_space_refine on Sun Aug 4 16:23:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qe5_18343/08_2024/8qe5_18343.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6957 2.51 5 N 1807 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ASP 1112": "OD1" <-> "OD2" Residue "A GLU 1275": "OE1" <-> "OE2" Residue "A PHE 1357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1466": "OD1" <-> "OD2" Residue "A ASP 1474": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10794 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10794 Classifications: {'peptide': 1340} Link IDs: {'PTRANS': 44, 'TRANS': 1295} Chain breaks: 6 Time building chain proxies: 6.67, per 1000 atoms: 0.62 Number of scatterers: 10794 At special positions: 0 Unit cell: (88.934, 104.036, 123.333, 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 58 16.00 O 1972 8.00 N 1807 7.00 C 6957 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 - 3.50 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: 3.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 60.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.638A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.784A pdb=" N ASN A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.753A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.970A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.723A pdb=" N ASN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 678 No H-bonds generated for 'chain 'A' and resid 676 through 678' Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.982A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 760 removed outlier: 3.702A pdb=" N ALA A 739 " --> pdb=" O MET A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.592A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.929A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.953A pdb=" N SER A 829 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 858 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 982 through 992 removed outlier: 4.102A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1043 Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1113 through 1126 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.714A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.623A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 4.008A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP A1195 " --> pdb=" O GLY A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.759A pdb=" N THR A1261 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1300 removed outlier: 3.679A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 removed outlier: 3.602A pdb=" N THR A1321 " --> pdb=" O LEU A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1330 removed outlier: 3.813A pdb=" N PHE A1330 " --> pdb=" O LEU A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1403 through 1412 removed outlier: 3.734A pdb=" N ARG A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.705A pdb=" N ASN A1439 " --> pdb=" O SER A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1456 Processing helix chain 'A' and resid 1458 through 1470 removed outlier: 3.559A pdb=" N TRP A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1546 removed outlier: 4.467A pdb=" N SER A1532 " --> pdb=" O PRO A1528 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL A1533 " --> pdb=" O ASP A1529 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A1543 " --> pdb=" O LYS A1539 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1546 " --> pdb=" O VAL A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 685 Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 833 through 837 removed outlier: 5.549A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 895 through 897 removed outlier: 4.076A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 924 through 925 Processing sheet with id=AB2, first strand: chain 'A' and resid 924 through 925 Processing sheet with id=AB3, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB4, first strand: chain 'A' and resid 1473 through 1479 removed outlier: 4.233A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1486 through 1490 removed outlier: 4.592A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1845 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: 4.17 Time building geometry restraints manager: 4.21 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: 3157 1.34 - 1.46: 1871 1.46 - 1.58: 5910 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 11035 Sorted by residual: bond pdb=" N THR A1321 " pdb=" CA THR A1321 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.14e+00 bond pdb=" N CYS A1456 " pdb=" CA CYS A1456 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.06e-02 8.90e+03 7.35e+00 bond pdb=" N PHE A1458 " pdb=" CA PHE A1458 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.09e+00 bond pdb=" N SER A1566 " pdb=" CA SER A1566 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.17e-02 7.31e+03 7.05e+00 bond pdb=" N PHE A1347 " pdb=" CA PHE A1347 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.27e-02 6.20e+03 6.75e+00 ... (remaining 11030 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.49: 255 106.49 - 113.45: 6021 113.45 - 120.40: 4168 120.40 - 127.35: 4357 127.35 - 134.31: 110 Bond angle restraints: 14911 Sorted by residual: angle pdb=" CA GLY A 767 " pdb=" C GLY A 767 " pdb=" O GLY A 767 " ideal model delta sigma weight residual 122.23 118.38 3.85 6.90e-01 2.10e+00 3.12e+01 angle pdb=" N LYS A1568 " pdb=" CA LYS A1568 " pdb=" C LYS A1568 " ideal model delta sigma weight residual 113.38 108.11 5.27 1.17e+00 7.31e-01 2.03e+01 angle pdb=" N SER A1569 " pdb=" CA SER A1569 " pdb=" C SER A1569 " ideal model delta sigma weight residual 113.21 108.89 4.32 1.15e+00 7.56e-01 1.41e+01 angle pdb=" C SER A 706 " pdb=" N ARG A 707 " pdb=" CA ARG A 707 " ideal model delta sigma weight residual 122.24 116.94 5.30 1.46e+00 4.69e-01 1.32e+01 angle pdb=" CA LYS A1344 " pdb=" C LYS A1344 " pdb=" O LYS A1344 " ideal model delta sigma weight residual 122.27 118.09 4.18 1.16e+00 7.43e-01 1.30e+01 ... (remaining 14906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5672 17.67 - 35.34: 689 35.34 - 53.00: 208 53.00 - 70.67: 50 70.67 - 88.34: 11 Dihedral angle restraints: 6630 sinusoidal: 2680 harmonic: 3950 Sorted by residual: dihedral pdb=" CA LEU A1152 " pdb=" C LEU A1152 " pdb=" N GLY A1153 " pdb=" CA GLY A1153 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP A 591 " pdb=" CB ASP A 591 " pdb=" CG ASP A 591 " pdb=" OD1 ASP A 591 " ideal model delta sinusoidal sigma weight residual -30.00 -87.37 57.37 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1107 0.035 - 0.070: 384 0.070 - 0.104: 126 0.104 - 0.139: 42 0.139 - 0.174: 6 Chirality restraints: 1665 Sorted by residual: chirality pdb=" CA LEU A1453 " pdb=" N LEU A1453 " pdb=" C LEU A1453 " pdb=" CB LEU A1453 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ILE A 812 " pdb=" N ILE A 812 " pdb=" C ILE A 812 " pdb=" CB ILE A 812 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA LEU A1449 " pdb=" N LEU A1449 " pdb=" C LEU A1449 " pdb=" CB LEU A1449 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1662 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 854 " 0.258 9.50e-02 1.11e+02 1.16e-01 8.25e+00 pdb=" NE ARG A 854 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 854 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 854 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 854 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1389 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO A1390 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A1390 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1390 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1044 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A1045 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1045 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1045 " -0.037 5.00e-02 4.00e+02 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 726 2.74 - 3.28: 10596 3.28 - 3.82: 19200 3.82 - 4.36: 23178 4.36 - 4.90: 38779 Nonbonded interactions: 92479 Sorted by model distance: nonbonded pdb=" OG1 THR A 459 " pdb=" OE1 GLN A1223 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR A 345 " pdb=" OD2 ASP A 348 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 341 " pdb=" OH TYR A 353 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A 624 " pdb=" NH2 ARG A 627 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR A1306 " pdb=" OD1 ASN A1434 " model vdw 2.267 3.040 ... (remaining 92474 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 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: 2.910 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.280 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.004 0.045 11035 Z= 0.258 Angle : 0.602 7.856 14911 Z= 0.374 Chirality : 0.042 0.174 1665 Planarity : 0.006 0.116 1873 Dihedral : 17.251 88.338 4070 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.85 % Allowed : 23.76 % Favored : 73.38 % 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: 1.17 (0.23), residues: 1326 helix: 1.54 (0.19), residues: 750 sheet: 0.86 (0.53), residues: 94 loop : -0.39 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.006 0.001 HIS A1413 PHE 0.018 0.002 PHE A1143 TYR 0.012 0.001 TYR A 599 ARG 0.016 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.6332 (ptp) cc_final: 0.6026 (ptp) REVERT: A 1086 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7395 (pm20) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 1.3815 time to fit residues: 292.5605 Evaluate side-chains 187 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1473 CYS Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 861 HIS A 936 GLN A1434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11035 Z= 0.200 Angle : 0.510 9.560 14911 Z= 0.270 Chirality : 0.040 0.147 1665 Planarity : 0.004 0.059 1873 Dihedral : 6.153 70.380 1495 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.03 % Allowed : 22.25 % Favored : 73.72 % 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: 1.54 (0.23), residues: 1326 helix: 1.92 (0.19), residues: 760 sheet: 0.36 (0.49), residues: 110 loop : -0.31 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.006 0.001 HIS A1413 PHE 0.018 0.002 PHE A1143 TYR 0.024 0.002 TYR A 599 ARG 0.005 0.000 ARG A1405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1086 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: A 1337 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 1418 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7564 (tpt170) outliers start: 48 outliers final: 17 residues processed: 208 average time/residue: 1.4177 time to fit residues: 316.0283 Evaluate side-chains 184 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 861 HIS A 936 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11035 Z= 0.221 Angle : 0.515 7.689 14911 Z= 0.272 Chirality : 0.040 0.147 1665 Planarity : 0.004 0.055 1873 Dihedral : 5.150 68.198 1459 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.11 % Allowed : 21.58 % Favored : 74.31 % 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: 1.61 (0.23), residues: 1326 helix: 1.99 (0.19), residues: 754 sheet: 0.83 (0.51), residues: 100 loop : -0.37 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.020 0.002 PHE A1143 TYR 0.025 0.002 TYR A 599 ARG 0.007 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 949 GLU cc_start: 0.6897 (tt0) cc_final: 0.6650 (tp30) REVERT: A 1086 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: A 1283 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.6836 (tmm) REVERT: A 1302 LYS cc_start: 0.7177 (tptp) cc_final: 0.6788 (tppt) REVERT: A 1337 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: A 1418 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7649 (tpt170) REVERT: A 1562 MET cc_start: 0.7854 (tmm) cc_final: 0.7517 (ttt) outliers start: 49 outliers final: 26 residues processed: 207 average time/residue: 1.2822 time to fit residues: 285.2942 Evaluate side-chains 199 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 571 ASN A 598 GLN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11035 Z= 0.158 Angle : 0.473 8.153 14911 Z= 0.249 Chirality : 0.038 0.145 1665 Planarity : 0.004 0.060 1873 Dihedral : 4.798 64.357 1458 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.78 % Allowed : 22.59 % Favored : 73.64 % 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: 1.72 (0.23), residues: 1326 helix: 2.14 (0.19), residues: 756 sheet: 0.33 (0.49), residues: 110 loop : -0.31 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A 474 PHE 0.015 0.001 PHE A1143 TYR 0.023 0.001 TYR A 599 ARG 0.006 0.000 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 ARG cc_start: 0.8531 (mpp80) cc_final: 0.8292 (mtt180) REVERT: A 949 GLU cc_start: 0.6936 (tt0) cc_final: 0.6687 (tp30) REVERT: A 1283 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.6836 (tmm) REVERT: A 1302 LYS cc_start: 0.7142 (tptp) cc_final: 0.6848 (tppt) REVERT: A 1320 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6126 (tt0) REVERT: A 1337 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: A 1418 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7496 (tpt170) REVERT: A 1449 LEU cc_start: 0.8726 (tt) cc_final: 0.8363 (tp) outliers start: 45 outliers final: 22 residues processed: 203 average time/residue: 1.3715 time to fit residues: 298.4737 Evaluate side-chains 192 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 674 ASN A 712 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 ASN A 936 GLN A1055 ASN A1575 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11035 Z= 0.347 Angle : 0.596 7.159 14911 Z= 0.314 Chirality : 0.044 0.156 1665 Planarity : 0.005 0.077 1873 Dihedral : 5.031 67.835 1452 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.95 % Allowed : 22.67 % Favored : 73.38 % 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: 1.38 (0.23), residues: 1326 helix: 1.82 (0.18), residues: 753 sheet: 0.79 (0.51), residues: 100 loop : -0.49 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 473 HIS 0.006 0.002 HIS A1096 PHE 0.026 0.003 PHE A1143 TYR 0.034 0.002 TYR A 599 ARG 0.012 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 949 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: A 1021 ARG cc_start: 0.6363 (mtt90) cc_final: 0.6134 (mtt90) REVERT: A 1086 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: A 1283 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: A 1302 LYS cc_start: 0.7134 (tptp) cc_final: 0.6882 (tppt) REVERT: A 1337 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: A 1418 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7860 (tpt170) outliers start: 47 outliers final: 27 residues processed: 197 average time/residue: 1.4061 time to fit residues: 297.1329 Evaluate side-chains 194 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 674 ASN A 861 HIS A 936 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11035 Z= 0.254 Angle : 0.547 8.720 14911 Z= 0.287 Chirality : 0.041 0.145 1665 Planarity : 0.005 0.068 1873 Dihedral : 4.914 66.895 1452 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.37 % Allowed : 22.08 % Favored : 73.55 % 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: 1.45 (0.23), residues: 1326 helix: 1.88 (0.18), residues: 754 sheet: 0.76 (0.50), residues: 100 loop : -0.49 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 473 HIS 0.005 0.001 HIS A 474 PHE 0.022 0.002 PHE A 259 TYR 0.030 0.002 TYR A 599 ARG 0.012 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 171 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 949 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: A 1021 ARG cc_start: 0.6372 (mtt90) cc_final: 0.6063 (mtt90) REVERT: A 1086 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: A 1283 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: A 1302 LYS cc_start: 0.7173 (tptp) cc_final: 0.6927 (tppt) REVERT: A 1337 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: A 1418 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7824 (tpt170) outliers start: 52 outliers final: 28 residues processed: 206 average time/residue: 1.1693 time to fit residues: 257.7093 Evaluate side-chains 200 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 129 optimal weight: 0.0370 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11035 Z= 0.164 Angle : 0.491 7.880 14911 Z= 0.257 Chirality : 0.039 0.143 1665 Planarity : 0.004 0.077 1873 Dihedral : 4.610 62.839 1452 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.86 % Allowed : 22.84 % Favored : 73.30 % 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: 1.66 (0.23), residues: 1326 helix: 2.12 (0.19), residues: 754 sheet: 0.24 (0.48), residues: 110 loop : -0.37 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 474 PHE 0.016 0.001 PHE A 259 TYR 0.031 0.001 TYR A 599 ARG 0.013 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 944 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7375 (mtp-110) REVERT: A 949 GLU cc_start: 0.6992 (tt0) cc_final: 0.6735 (tp30) REVERT: A 1021 ARG cc_start: 0.6317 (mtt90) cc_final: 0.6004 (mtt90) REVERT: A 1086 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: A 1283 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.6875 (tmm) REVERT: A 1320 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: A 1337 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: A 1418 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7458 (tpt170) outliers start: 46 outliers final: 26 residues processed: 202 average time/residue: 1.3014 time to fit residues: 282.3960 Evaluate side-chains 200 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 82 optimal weight: 0.0770 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 674 ASN A1055 ASN A1096 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11035 Z= 0.143 Angle : 0.486 7.599 14911 Z= 0.254 Chirality : 0.038 0.144 1665 Planarity : 0.004 0.080 1873 Dihedral : 4.382 59.681 1452 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.02 % Allowed : 24.10 % Favored : 72.88 % 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: 1.76 (0.23), residues: 1326 helix: 2.24 (0.19), residues: 759 sheet: 0.13 (0.47), residues: 116 loop : -0.39 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.013 0.001 PHE A1143 TYR 0.032 0.001 TYR A 599 ARG 0.014 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 949 GLU cc_start: 0.6939 (tt0) cc_final: 0.6670 (tp30) REVERT: A 1086 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: A 1283 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.6850 (tmm) REVERT: A 1320 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6198 (tt0) REVERT: A 1337 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 1418 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7441 (tpt170) REVERT: A 1449 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8404 (tp) outliers start: 36 outliers final: 24 residues processed: 197 average time/residue: 1.3176 time to fit residues: 278.6580 Evaluate side-chains 200 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 0.0020 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 674 ASN A 936 GLN A1055 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11035 Z= 0.190 Angle : 0.516 7.432 14911 Z= 0.270 Chirality : 0.040 0.144 1665 Planarity : 0.004 0.069 1873 Dihedral : 4.551 62.359 1452 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.11 % Allowed : 23.93 % Favored : 72.96 % 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: 1.67 (0.23), residues: 1326 helix: 2.12 (0.18), residues: 763 sheet: 0.18 (0.47), residues: 121 loop : -0.41 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.018 0.002 PHE A 259 TYR 0.030 0.001 TYR A 599 ARG 0.015 0.001 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 949 GLU cc_start: 0.6970 (tt0) cc_final: 0.6698 (tp30) REVERT: A 1086 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: A 1283 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.6935 (tmm) REVERT: A 1302 LYS cc_start: 0.7464 (ttpp) cc_final: 0.7103 (tppt) REVERT: A 1320 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6227 (tt0) REVERT: A 1337 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: A 1418 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7492 (tpt170) REVERT: A 1449 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8426 (tp) outliers start: 37 outliers final: 25 residues processed: 191 average time/residue: 1.3048 time to fit residues: 268.4906 Evaluate side-chains 196 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1320 GLU Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 674 ASN A1324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11035 Z= 0.258 Angle : 0.564 7.350 14911 Z= 0.296 Chirality : 0.042 0.147 1665 Planarity : 0.004 0.068 1873 Dihedral : 4.808 63.288 1452 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.36 % Allowed : 23.76 % Favored : 72.88 % 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: 1.51 (0.23), residues: 1326 helix: 1.98 (0.18), residues: 757 sheet: 0.18 (0.47), residues: 120 loop : -0.42 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.006 0.001 HIS A1413 PHE 0.021 0.002 PHE A 259 TYR 0.032 0.002 TYR A 599 ARG 0.013 0.001 ARG A 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 949 GLU cc_start: 0.7029 (tt0) cc_final: 0.6737 (tp30) REVERT: A 1086 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: A 1283 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.6866 (tmm) REVERT: A 1302 LYS cc_start: 0.7491 (ttpp) cc_final: 0.7144 (tppt) REVERT: A 1337 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: A 1418 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7628 (tpt170) REVERT: A 1449 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8516 (tp) outliers start: 40 outliers final: 28 residues processed: 190 average time/residue: 1.3172 time to fit residues: 268.8028 Evaluate side-chains 197 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 ARG Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 598 GLN A 674 ASN A 936 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.158965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129953 restraints weight = 10796.525| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.49 r_work: 0.3126 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11035 Z= 0.188 Angle : 0.525 8.701 14911 Z= 0.276 Chirality : 0.040 0.144 1665 Planarity : 0.004 0.058 1873 Dihedral : 4.630 60.740 1452 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.94 % Allowed : 24.27 % Favored : 72.80 % 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: 1.61 (0.23), residues: 1326 helix: 2.07 (0.18), residues: 755 sheet: 0.17 (0.46), residues: 120 loop : -0.37 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.017 0.002 PHE A1143 TYR 0.039 0.002 TYR A 599 ARG 0.009 0.001 ARG A 707 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4819.85 seconds wall clock time: 84 minutes 57.75 seconds (5097.75 seconds total)