Starting phenix.real_space_refine on Sat Aug 23 08:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_18343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_18343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_18343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_18343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qe5_18343/08_2025/8qe5_18343.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.37, per 1000 atoms: 0.22 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 - 3.00 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: 0.94 Conformation dependent library (CDL) restraints added in 426.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 2.13 Time building geometry restraints manager: 1.20 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: 0.00 - 1.57: 14431 1.57 - 3.14: 413 3.14 - 4.71: 54 4.71 - 6.28: 11 6.28 - 7.86: 2 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- 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= 0.238 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 : 7.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.016 0.001 ARG A 707 TYR 0.012 0.001 TYR A 599 PHE 0.018 0.002 PHE A1143 TRP 0.018 0.002 TRP A 473 HIS 0.006 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00399 (11035) covalent geometry : angle 0.60155 (14911) hydrogen bonds : bond 0.12537 ( 624) hydrogen bonds : angle 5.79494 ( 1845) *********************** 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 to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.263 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: 0.5671 time to fit residues: 119.5719 Evaluate side-chains 187 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0040 chunk 55 optimal weight: 0.8980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 861 HIS A 936 GLN A1434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.160051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.130743 restraints weight = 10904.131| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.21 r_work: 0.3147 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11035 Z= 0.112 Angle : 0.483 9.884 14911 Z= 0.255 Chirality : 0.039 0.146 1665 Planarity : 0.004 0.058 1873 Dihedral : 5.908 68.987 1495 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.86 % Allowed : 22.33 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.23), residues: 1326 helix: 2.03 (0.19), residues: 760 sheet: 0.35 (0.49), residues: 111 loop : -0.30 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1405 TYR 0.021 0.001 TYR A 599 PHE 0.015 0.001 PHE A1143 TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00242 (11035) covalent geometry : angle 0.48275 (14911) hydrogen bonds : bond 0.04150 ( 624) hydrogen bonds : angle 4.60752 ( 1845) *********************** 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 228 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8207 (pt) REVERT: A 645 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: A 1337 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: A 1418 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7606 (tpt170) outliers start: 46 outliers final: 15 residues processed: 209 average time/residue: 0.5585 time to fit residues: 124.2396 Evaluate side-chains 186 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 645 GLU 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 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 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129546 restraints weight = 10845.314| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.20 r_work: 0.3114 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11035 Z= 0.152 Angle : 0.514 7.664 14911 Z= 0.271 Chirality : 0.040 0.146 1665 Planarity : 0.004 0.054 1873 Dihedral : 4.972 67.766 1456 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.95 % Allowed : 21.91 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1326 helix: 2.02 (0.19), residues: 755 sheet: 0.34 (0.49), residues: 110 loop : -0.29 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1405 TYR 0.013 0.002 TYR A 599 PHE 0.020 0.002 PHE A1143 TRP 0.017 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00348 (11035) covalent geometry : angle 0.51402 (14911) hydrogen bonds : bond 0.04687 ( 624) hydrogen bonds : angle 4.57450 ( 1845) *********************** 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 219 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1021 ARG cc_start: 0.6280 (mtt90) cc_final: 0.5868 (mtt90) REVERT: A 1086 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: A 1283 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.6714 (tmm) REVERT: A 1302 LYS cc_start: 0.7268 (tptp) cc_final: 0.6740 (tppt) REVERT: A 1337 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: A 1418 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7601 (tpt170) outliers start: 47 outliers final: 25 residues processed: 199 average time/residue: 0.5982 time to fit residues: 127.5657 Evaluate side-chains 197 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 331 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 358 GLN 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 949 GLU 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 60 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 571 ASN A 598 GLN A 674 ASN A 861 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130480 restraints weight = 10895.028| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.39 r_work: 0.3133 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0918 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= 0.119 Angle : 0.484 8.295 14911 Z= 0.254 Chirality : 0.039 0.150 1665 Planarity : 0.004 0.051 1873 Dihedral : 4.741 65.010 1455 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.23), residues: 1326 helix: 2.12 (0.19), residues: 756 sheet: 0.32 (0.49), residues: 110 loop : -0.30 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 707 TYR 0.020 0.001 TYR A 599 PHE 0.016 0.001 PHE A1143 TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00266 (11035) covalent geometry : angle 0.48352 (14911) hydrogen bonds : bond 0.04149 ( 624) hydrogen bonds : angle 4.44016 ( 1845) *********************** 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 to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7772 (ptm-80) REVERT: A 975 LYS cc_start: 0.8934 (tttp) cc_final: 0.8693 (ttpp) REVERT: A 1086 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: A 1283 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.6662 (tmm) REVERT: A 1302 LYS cc_start: 0.7208 (tptp) cc_final: 0.6755 (tppt) REVERT: A 1320 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5942 (tt0) REVERT: A 1337 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: A 1418 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7629 (tpt170) REVERT: A 1449 LEU cc_start: 0.8545 (tt) cc_final: 0.8103 (tp) outliers start: 45 outliers final: 22 residues processed: 203 average time/residue: 0.5563 time to fit residues: 120.9637 Evaluate side-chains 195 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 949 GLU 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 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 133 optimal weight: 0.0470 chunk 80 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 674 ASN A 766 ASN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129296 restraints weight = 10831.278| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.19 r_work: 0.3130 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0960 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= 0.150 Angle : 0.514 7.333 14911 Z= 0.270 Chirality : 0.040 0.145 1665 Planarity : 0.004 0.062 1873 Dihedral : 4.875 65.582 1455 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.69 % Allowed : 22.50 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1326 helix: 2.04 (0.19), residues: 758 sheet: 0.31 (0.49), residues: 110 loop : -0.34 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 707 TYR 0.029 0.002 TYR A 599 PHE 0.020 0.002 PHE A1143 TRP 0.018 0.002 TRP A 473 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00345 (11035) covalent geometry : angle 0.51378 (14911) hydrogen bonds : bond 0.04553 ( 624) hydrogen bonds : angle 4.48180 ( 1845) *********************** 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 219 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: A 975 LYS cc_start: 0.8935 (tttp) cc_final: 0.8711 (ttpp) REVERT: A 1021 ARG cc_start: 0.6145 (mtt90) cc_final: 0.5771 (mtt90) REVERT: A 1086 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 1283 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.6679 (tmm) REVERT: A 1302 LYS cc_start: 0.7239 (tptp) cc_final: 0.6836 (tppt) REVERT: A 1337 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: A 1418 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7616 (tpt170) REVERT: A 1449 LEU cc_start: 0.8558 (tt) cc_final: 0.8181 (tp) outliers start: 44 outliers final: 25 residues processed: 202 average time/residue: 0.6241 time to fit residues: 134.7540 Evaluate side-chains 198 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 MET 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 778 GLU Chi-restraints excluded: chain A residue 1012 VAL 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 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 53 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 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 565 ASN A 598 GLN A 674 ASN A 861 HIS A 936 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128920 restraints weight = 10813.598| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.40 r_work: 0.3102 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11035 Z= 0.149 Angle : 0.523 7.286 14911 Z= 0.275 Chirality : 0.040 0.144 1665 Planarity : 0.004 0.068 1873 Dihedral : 4.897 65.095 1455 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.03 % Allowed : 22.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1326 helix: 2.06 (0.19), residues: 757 sheet: 0.77 (0.51), residues: 100 loop : -0.42 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 707 TYR 0.030 0.002 TYR A 599 PHE 0.020 0.002 PHE A1143 TRP 0.018 0.002 TRP A 473 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00342 (11035) covalent geometry : angle 0.52298 (14911) hydrogen bonds : bond 0.04529 ( 624) hydrogen bonds : angle 4.48374 ( 1845) *********************** 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 219 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: A 944 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7612 (mtp-110) REVERT: A 975 LYS cc_start: 0.8957 (tttp) cc_final: 0.8712 (ttpp) REVERT: A 1021 ARG cc_start: 0.6191 (mtt90) cc_final: 0.5812 (mtt90) REVERT: A 1086 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: A 1283 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.6701 (tmm) REVERT: A 1302 LYS cc_start: 0.7358 (tptp) cc_final: 0.6976 (tppt) REVERT: A 1337 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 1408 MET cc_start: 0.7829 (mtm) cc_final: 0.7281 (mtp) REVERT: A 1418 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7665 (tpt170) outliers start: 48 outliers final: 26 residues processed: 204 average time/residue: 0.6986 time to fit residues: 152.2101 Evaluate side-chains 194 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 674 ASN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.159524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131270 restraints weight = 10832.522| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.26 r_work: 0.3118 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1061 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= 0.118 Angle : 0.498 9.269 14911 Z= 0.260 Chirality : 0.039 0.144 1665 Planarity : 0.004 0.085 1873 Dihedral : 4.708 63.034 1455 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.53 % Allowed : 23.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.23), residues: 1326 helix: 2.14 (0.19), residues: 762 sheet: 0.17 (0.47), residues: 121 loop : -0.38 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 707 TYR 0.035 0.001 TYR A 599 PHE 0.016 0.001 PHE A1143 TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00263 (11035) covalent geometry : angle 0.49793 (14911) hydrogen bonds : bond 0.04044 ( 624) hydrogen bonds : angle 4.36746 ( 1845) *********************** 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 216 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7823 (ptm-80) REVERT: A 707 ARG cc_start: 0.7978 (ptt90) cc_final: 0.7761 (ppt170) REVERT: A 778 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 944 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7765 (mtp-110) REVERT: A 975 LYS cc_start: 0.8964 (tttp) cc_final: 0.8705 (ttpp) REVERT: A 1283 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.6701 (tmm) REVERT: A 1302 LYS cc_start: 0.7320 (tptp) cc_final: 0.6961 (tppt) REVERT: A 1337 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 1418 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7483 (tpt170) outliers start: 42 outliers final: 25 residues processed: 200 average time/residue: 0.6361 time to fit residues: 136.0827 Evaluate side-chains 197 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 449 THR Chi-restraints excluded: chain A residue 450 VAL 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 778 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1012 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 674 ASN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.157530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.128175 restraints weight = 10878.639| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.33 r_work: 0.3083 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11035 Z= 0.170 Angle : 0.551 7.624 14911 Z= 0.289 Chirality : 0.042 0.147 1665 Planarity : 0.004 0.067 1873 Dihedral : 4.786 64.461 1452 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.61 % Allowed : 23.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.23), residues: 1326 helix: 2.02 (0.18), residues: 755 sheet: 0.63 (0.49), residues: 110 loop : -0.41 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 707 TYR 0.032 0.002 TYR A 599 PHE 0.022 0.002 PHE A 259 TRP 0.019 0.002 TRP A 473 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00397 (11035) covalent geometry : angle 0.55134 (14911) hydrogen bonds : bond 0.04767 ( 624) hydrogen bonds : angle 4.52214 ( 1845) *********************** 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 208 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 778 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 975 LYS cc_start: 0.8980 (tttp) cc_final: 0.8718 (ttpp) REVERT: A 1021 ARG cc_start: 0.6301 (mtt90) cc_final: 0.6031 (mtt90) REVERT: A 1283 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6694 (tmm) REVERT: A 1302 LYS cc_start: 0.7356 (tptp) cc_final: 0.7068 (tppt) REVERT: A 1337 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: A 1418 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7798 (tpt170) REVERT: A 1449 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8267 (tp) outliers start: 43 outliers final: 28 residues processed: 196 average time/residue: 0.6101 time to fit residues: 128.0096 Evaluate side-chains 193 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 449 THR Chi-restraints excluded: chain A residue 450 VAL 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 778 GLU 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 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 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 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 102 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 674 ASN A 861 HIS A 936 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.158305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129535 restraints weight = 10894.650| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.34 r_work: 0.3088 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1060 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= 0.146 Angle : 0.534 7.410 14911 Z= 0.280 Chirality : 0.041 0.145 1665 Planarity : 0.005 0.097 1873 Dihedral : 4.721 62.986 1452 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.23), residues: 1326 helix: 2.04 (0.18), residues: 755 sheet: 0.19 (0.47), residues: 120 loop : -0.37 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 707 TYR 0.042 0.002 TYR A 599 PHE 0.019 0.002 PHE A1143 TRP 0.018 0.002 TRP A 473 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00336 (11035) covalent geometry : angle 0.53445 (14911) hydrogen bonds : bond 0.04464 ( 624) hydrogen bonds : angle 4.46678 ( 1845) *********************** 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 205 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 778 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 975 LYS cc_start: 0.8975 (tttp) cc_final: 0.8718 (ttpp) REVERT: A 1021 ARG cc_start: 0.6291 (mtt90) cc_final: 0.6001 (mtt90) REVERT: A 1283 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.6716 (tmm) REVERT: A 1337 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: A 1418 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7588 (tpt170) REVERT: A 1449 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8193 (tp) outliers start: 40 outliers final: 30 residues processed: 192 average time/residue: 0.6840 time to fit residues: 140.9405 Evaluate side-chains 200 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 273 SER 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 449 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 468 LYS 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 778 GLU Chi-restraints excluded: chain A residue 800 VAL 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 1114 THR Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain A residue 1216 LEU 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 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 89 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 598 GLN A 674 ASN A 861 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129792 restraints weight = 10880.224| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.47 r_work: 0.3131 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11035 Z= 0.127 Angle : 0.521 7.348 14911 Z= 0.272 Chirality : 0.040 0.144 1665 Planarity : 0.004 0.085 1873 Dihedral : 4.588 60.650 1452 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.27 % Allowed : 24.35 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1326 helix: 2.09 (0.19), residues: 757 sheet: 0.23 (0.47), residues: 120 loop : -0.37 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 707 TYR 0.033 0.001 TYR A 599 PHE 0.017 0.002 PHE A1143 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00288 (11035) covalent geometry : angle 0.52056 (14911) hydrogen bonds : bond 0.04195 ( 624) hydrogen bonds : angle 4.38999 ( 1845) ********************** 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 206 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 778 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 975 LYS cc_start: 0.8939 (tttp) cc_final: 0.8679 (ttpp) REVERT: A 1021 ARG cc_start: 0.6195 (mtt90) cc_final: 0.5897 (mtt90) REVERT: A 1283 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.6677 (tmm) REVERT: A 1337 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 1418 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7438 (tpt170) REVERT: A 1449 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8130 (tp) outliers start: 39 outliers final: 27 residues processed: 195 average time/residue: 0.7019 time to fit residues: 146.7652 Evaluate side-chains 198 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 273 SER 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 449 THR Chi-restraints excluded: chain A residue 450 VAL 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 714 ARG Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 778 GLU 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 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 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 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 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 565 ASN A 674 ASN A 861 HIS A 936 GLN A1055 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.159238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129693 restraints weight = 10872.859| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.25 r_work: 0.3144 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1138 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= 0.125 Angle : 0.515 8.466 14911 Z= 0.269 Chirality : 0.040 0.147 1665 Planarity : 0.004 0.070 1873 Dihedral : 4.558 59.521 1452 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 24.52 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1326 helix: 2.09 (0.18), residues: 758 sheet: 0.25 (0.47), residues: 120 loop : -0.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 707 TYR 0.029 0.001 TYR A 599 PHE 0.017 0.001 PHE A1143 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd covalent geometry : bond 0.00283 (11035) covalent geometry : angle 0.51549 (14911) hydrogen bonds : bond 0.04166 ( 624) hydrogen bonds : angle 4.38279 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.69 seconds wall clock time: 73 minutes 11.02 seconds (4391.02 seconds total)