Starting phenix.real_space_refine on Tue May 13 19:20:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4t_16428/05_2025/8c4t_16428.cif" } resolution = 3.23 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6683 2.51 5 N 1757 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10459 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10199 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1227} Chain breaks: 12 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.13, per 1000 atoms: 0.59 Number of scatterers: 10459 At special positions: 0 Unit cell: (96.18, 100.76, 120.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 12 15.00 Mg 1 11.99 O 1950 8.00 N 1757 7.00 C 6683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 59.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.550A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.960A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.768A 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 352 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.404A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.634A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) 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: 3.837A 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 648 Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.699A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.831A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 760 removed outlier: 3.555A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.808A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.613A pdb=" N LYS A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 847 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 918 removed outlier: 4.282A pdb=" N ASN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 removed outlier: 4.567A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 removed outlier: 4.077A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.800A 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 1042 Processing helix chain 'A' and resid 1062 through 1084 Processing helix chain 'A' and resid 1116 through 1126 Processing helix chain 'A' and resid 1128 through 1134 removed outlier: 3.914A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.911A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1195 removed outlier: 4.502A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.879A pdb=" N GLN A1255 " --> pdb=" O ALA A1251 " (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 1298 removed outlier: 3.760A pdb=" N LEU A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 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 1396 Processing helix chain 'A' and resid 1403 through 1412 removed outlier: 4.383A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A1410 " --> pdb=" O PHE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1464 through 1471 Processing helix chain 'A' and resid 1503 through 1511 removed outlier: 3.575A pdb=" N ILE A1507 " --> pdb=" O ILE A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1552 through 1560 Processing helix chain 'A' and resid 1583 through 1593 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.535A pdb=" N TYR A 637 " --> pdb=" O VAL A1164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 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 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 833 through 837 removed outlier: 4.532A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.214A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AA9, first strand: chain 'A' and resid 1169 through 1171 Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 3.572A pdb=" N ASP A1474 " --> pdb=" O ARG A1600 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1489 593 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1654 1.29 - 1.42: 2895 1.42 - 1.55: 6043 1.55 - 1.68: 23 1.68 - 1.82: 93 Bond restraints: 10708 Sorted by residual: bond pdb=" C ILE A 572 " pdb=" O ILE A 572 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.19e-02 7.06e+03 4.91e+01 bond pdb=" C GLU A 575 " pdb=" O GLU A 575 " ideal model delta sigma weight residual 1.236 1.168 0.069 1.22e-02 6.72e+03 3.16e+01 bond pdb=" CA ALA A 573 " pdb=" CB ALA A 573 " ideal model delta sigma weight residual 1.534 1.455 0.079 1.71e-02 3.42e+03 2.11e+01 bond pdb=" N ILE A1183 " pdb=" CA ILE A1183 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.95e+01 bond pdb=" C ALA A 573 " pdb=" O ALA A 573 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.34e-02 5.57e+03 1.63e+01 ... (remaining 10703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14299 1.95 - 3.89: 174 3.89 - 5.84: 30 5.84 - 7.78: 11 7.78 - 9.73: 5 Bond angle restraints: 14519 Sorted by residual: angle pdb=" N GLU A 575 " pdb=" CA GLU A 575 " pdb=" CB GLU A 575 " ideal model delta sigma weight residual 110.20 101.89 8.31 1.49e+00 4.50e-01 3.11e+01 angle pdb=" CA ILE A 572 " pdb=" C ILE A 572 " pdb=" O ILE A 572 " ideal model delta sigma weight residual 120.78 114.30 6.48 1.25e+00 6.40e-01 2.69e+01 angle pdb=" C ILE A 572 " pdb=" CA ILE A 572 " pdb=" CB ILE A 572 " ideal model delta sigma weight residual 111.29 103.93 7.36 1.64e+00 3.72e-01 2.01e+01 angle pdb=" C3' A C 5 " pdb=" C2' A C 5 " pdb=" O2' A C 5 " ideal model delta sigma weight residual 110.70 117.36 -6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" CA GLN A1575 " pdb=" C GLN A1575 " pdb=" O GLN A1575 " ideal model delta sigma weight residual 121.82 116.57 5.25 1.21e+00 6.83e-01 1.88e+01 ... (remaining 14514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 6045 29.13 - 58.25: 351 58.25 - 87.37: 27 87.37 - 116.50: 1 116.50 - 145.62: 1 Dihedral angle restraints: 6425 sinusoidal: 2696 harmonic: 3729 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 54.38 145.62 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -160.00 -65.74 -94.26 1 1.50e+01 4.44e-03 4.58e+01 dihedral pdb=" C VAL A1578 " pdb=" N VAL A1578 " pdb=" CA VAL A1578 " pdb=" CB VAL A1578 " ideal model delta harmonic sigma weight residual -122.00 -135.04 13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 6422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1595 0.111 - 0.222: 29 0.222 - 0.334: 7 0.334 - 0.445: 1 0.445 - 0.556: 1 Chirality restraints: 1633 Sorted by residual: chirality pdb=" P A C 2 " pdb=" OP1 A C 2 " pdb=" OP2 A C 2 " pdb=" O5' A C 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.85 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" CA VAL A1578 " pdb=" N VAL A1578 " pdb=" C VAL A1578 " pdb=" CB VAL A1578 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB VAL A1578 " pdb=" CA VAL A1578 " pdb=" CG1 VAL A1578 " pdb=" CG2 VAL A1578 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1630 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 573 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ALA A 573 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 573 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 574 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 571 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN A 571 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 571 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 572 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1574 " 0.009 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C VAL A1574 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL A1574 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A1575 " 0.012 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 242 2.70 - 3.25: 10204 3.25 - 3.80: 17062 3.80 - 4.35: 22353 4.35 - 4.90: 37668 Nonbonded interactions: 87529 Sorted by model distance: nonbonded pdb=" OH TYR A 341 " pdb=" OH TYR A 353 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OE2 GLU A 870 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU A 275 " pdb=" OH TYR A 661 " model vdw 2.262 3.040 nonbonded pdb=" O ARG A 714 " pdb=" OG SER A 718 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 242 " pdb=" NH2 ARG A 774 " model vdw 2.267 3.120 ... (remaining 87524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.003 0.083 10708 Z= 0.210 Angle : 0.580 9.729 14519 Z= 0.333 Chirality : 0.047 0.556 1633 Planarity : 0.004 0.046 1779 Dihedral : 16.975 145.624 4005 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.36 % Allowed : 22.05 % Favored : 77.59 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1242 helix: 1.48 (0.19), residues: 695 sheet: -0.43 (0.52), residues: 87 loop : -0.78 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.010 0.001 TYR A1306 ARG 0.005 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.14139 ( 583) hydrogen bonds : angle 5.82339 ( 1692) covalent geometry : bond 0.00345 (10708) covalent geometry : angle 0.58027 (14519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 1.107 Fit side-chains REVERT: A 575 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: A 1577 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7408 (p0) outliers start: 4 outliers final: 1 residues processed: 134 average time/residue: 0.2316 time to fit residues: 43.9154 Evaluate side-chains 123 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1577 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 HIS A 858 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 GLN A1434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111876 restraints weight = 12901.149| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.81 r_work: 0.3018 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10708 Z= 0.184 Angle : 0.528 9.872 14519 Z= 0.274 Chirality : 0.040 0.198 1633 Planarity : 0.004 0.037 1779 Dihedral : 9.876 142.697 1548 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.95 % Allowed : 20.45 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1242 helix: 1.59 (0.19), residues: 712 sheet: -0.44 (0.51), residues: 95 loop : -0.82 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.020 0.002 PHE A 585 TYR 0.012 0.001 TYR A 352 ARG 0.004 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 583) hydrogen bonds : angle 4.47047 ( 1692) covalent geometry : bond 0.00436 (10708) covalent geometry : angle 0.52842 (14519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 774 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8055 (mtt-85) outliers start: 33 outliers final: 18 residues processed: 159 average time/residue: 0.2616 time to fit residues: 59.4212 Evaluate side-chains 143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114745 restraints weight = 13082.221| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.80 r_work: 0.3075 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10708 Z= 0.123 Angle : 0.467 8.679 14519 Z= 0.242 Chirality : 0.037 0.194 1633 Planarity : 0.003 0.042 1779 Dihedral : 9.461 143.176 1543 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.86 % Allowed : 20.71 % Favored : 76.43 % 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: 1.10 (0.23), residues: 1242 helix: 1.78 (0.19), residues: 709 sheet: -0.34 (0.51), residues: 99 loop : -0.76 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.013 0.001 TYR A1509 ARG 0.002 0.000 ARG A1427 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 583) hydrogen bonds : angle 4.19090 ( 1692) covalent geometry : bond 0.00281 (10708) covalent geometry : angle 0.46656 (14519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8095 (t0) cc_final: 0.7886 (t0) REVERT: A 774 ARG cc_start: 0.8603 (ttm110) cc_final: 0.8184 (mtt-85) REVERT: A 855 TYR cc_start: 0.8617 (t80) cc_final: 0.8325 (t80) REVERT: A 1057 LEU cc_start: 0.8779 (mt) cc_final: 0.8368 (mp) REVERT: A 1305 LEU cc_start: 0.8622 (tp) cc_final: 0.8413 (tt) outliers start: 32 outliers final: 18 residues processed: 161 average time/residue: 0.2402 time to fit residues: 55.0476 Evaluate side-chains 145 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111175 restraints weight = 13012.560| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.79 r_work: 0.3005 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10708 Z= 0.191 Angle : 0.519 9.737 14519 Z= 0.267 Chirality : 0.039 0.210 1633 Planarity : 0.004 0.046 1779 Dihedral : 9.465 141.556 1543 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.66 % Allowed : 19.73 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1242 helix: 1.65 (0.19), residues: 710 sheet: -0.34 (0.50), residues: 100 loop : -0.76 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.021 0.002 PHE A 585 TYR 0.015 0.001 TYR A 352 ARG 0.002 0.000 ARG A1238 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 583) hydrogen bonds : angle 4.22203 ( 1692) covalent geometry : bond 0.00461 (10708) covalent geometry : angle 0.51949 (14519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8038 (t0) cc_final: 0.7814 (t0) REVERT: A 774 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8055 (mtt-85) REVERT: A 926 TYR cc_start: 0.6837 (m-10) cc_final: 0.6582 (m-10) outliers start: 41 outliers final: 31 residues processed: 162 average time/residue: 0.2406 time to fit residues: 54.5994 Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114001 restraints weight = 12839.139| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.72 r_work: 0.3028 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10708 Z= 0.134 Angle : 0.486 9.054 14519 Z= 0.249 Chirality : 0.038 0.187 1633 Planarity : 0.004 0.050 1779 Dihedral : 9.379 142.390 1543 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 20.71 % Favored : 75.98 % 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: 1.15 (0.23), residues: 1242 helix: 1.82 (0.19), residues: 704 sheet: -0.38 (0.50), residues: 100 loop : -0.68 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.014 0.001 TYR A1509 ARG 0.002 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 583) hydrogen bonds : angle 4.10667 ( 1692) covalent geometry : bond 0.00315 (10708) covalent geometry : angle 0.48595 (14519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7995 (t0) cc_final: 0.7770 (t0) REVERT: A 461 LYS cc_start: 0.8748 (tttt) cc_final: 0.8389 (tptt) REVERT: A 774 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8095 (mtt-85) REVERT: A 926 TYR cc_start: 0.6780 (m-10) cc_final: 0.6529 (m-10) REVERT: A 1057 LEU cc_start: 0.8789 (mt) cc_final: 0.8329 (mp) outliers start: 37 outliers final: 28 residues processed: 160 average time/residue: 0.2200 time to fit residues: 50.0822 Evaluate side-chains 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113472 restraints weight = 13025.378| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.80 r_work: 0.3047 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10708 Z= 0.147 Angle : 0.494 9.044 14519 Z= 0.253 Chirality : 0.038 0.174 1633 Planarity : 0.004 0.055 1779 Dihedral : 9.334 142.486 1543 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.84 % Allowed : 20.45 % Favored : 75.71 % 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: 1.15 (0.23), residues: 1242 helix: 1.83 (0.19), residues: 704 sheet: -0.41 (0.50), residues: 100 loop : -0.70 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.018 0.001 PHE A 585 TYR 0.016 0.001 TYR A1509 ARG 0.003 0.000 ARG A1558 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 583) hydrogen bonds : angle 4.10068 ( 1692) covalent geometry : bond 0.00347 (10708) covalent geometry : angle 0.49399 (14519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8814 (tttt) cc_final: 0.8498 (tptt) REVERT: A 926 TYR cc_start: 0.6918 (m-10) cc_final: 0.6641 (m-10) REVERT: A 991 MET cc_start: 0.9037 (tpp) cc_final: 0.8815 (tpp) REVERT: A 1057 LEU cc_start: 0.8789 (mt) cc_final: 0.8358 (mp) REVERT: A 1451 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7471 (mm-40) outliers start: 43 outliers final: 32 residues processed: 159 average time/residue: 0.2279 time to fit residues: 51.8507 Evaluate side-chains 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 118 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115002 restraints weight = 13085.577| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.82 r_work: 0.3042 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10708 Z= 0.111 Angle : 0.474 9.227 14519 Z= 0.241 Chirality : 0.037 0.174 1633 Planarity : 0.004 0.053 1779 Dihedral : 9.208 144.063 1543 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.95 % Allowed : 21.52 % Favored : 75.54 % 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: 1.29 (0.23), residues: 1242 helix: 1.97 (0.19), residues: 701 sheet: -0.41 (0.50), residues: 100 loop : -0.66 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.017 0.001 TYR A1509 ARG 0.003 0.000 ARG A1558 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 583) hydrogen bonds : angle 3.98757 ( 1692) covalent geometry : bond 0.00253 (10708) covalent geometry : angle 0.47414 (14519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8838 (tttt) cc_final: 0.8406 (tptt) REVERT: A 774 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8063 (mtt-85) REVERT: A 1304 MET cc_start: 0.7823 (mmt) cc_final: 0.7474 (mmm) REVERT: A 1503 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (mt) outliers start: 33 outliers final: 24 residues processed: 154 average time/residue: 0.2310 time to fit residues: 50.4257 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111198 restraints weight = 13058.309| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.80 r_work: 0.3039 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10708 Z= 0.205 Angle : 0.538 9.733 14519 Z= 0.275 Chirality : 0.040 0.176 1633 Planarity : 0.004 0.054 1779 Dihedral : 9.326 141.917 1543 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.39 % Allowed : 20.98 % Favored : 75.62 % 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: 1.06 (0.23), residues: 1242 helix: 1.76 (0.19), residues: 703 sheet: -0.42 (0.50), residues: 100 loop : -0.75 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.022 0.002 PHE A 585 TYR 0.018 0.002 TYR A1509 ARG 0.002 0.000 ARG A1238 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 583) hydrogen bonds : angle 4.16440 ( 1692) covalent geometry : bond 0.00496 (10708) covalent geometry : angle 0.53821 (14519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8894 (tttt) cc_final: 0.8561 (tptt) REVERT: A 926 TYR cc_start: 0.6886 (m-10) cc_final: 0.6639 (m-10) REVERT: A 1304 MET cc_start: 0.7915 (mmt) cc_final: 0.7569 (mmm) REVERT: A 1451 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7430 (mm-40) REVERT: A 1503 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 1556 MET cc_start: 0.8780 (tpp) cc_final: 0.8578 (tpp) outliers start: 38 outliers final: 30 residues processed: 157 average time/residue: 0.2271 time to fit residues: 50.7570 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114093 restraints weight = 13059.753| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.80 r_work: 0.3072 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10708 Z= 0.109 Angle : 0.473 9.206 14519 Z= 0.242 Chirality : 0.037 0.167 1633 Planarity : 0.004 0.054 1779 Dihedral : 9.189 144.091 1543 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.32 % Allowed : 22.23 % Favored : 75.45 % 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: 1.23 (0.23), residues: 1242 helix: 1.93 (0.19), residues: 703 sheet: -0.38 (0.50), residues: 100 loop : -0.72 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.019 0.001 TYR A1509 ARG 0.002 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 583) hydrogen bonds : angle 3.99523 ( 1692) covalent geometry : bond 0.00243 (10708) covalent geometry : angle 0.47326 (14519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8909 (tttt) cc_final: 0.8538 (tptt) REVERT: A 1304 MET cc_start: 0.7916 (mmt) cc_final: 0.7584 (mmm) REVERT: A 1451 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7443 (mm-40) REVERT: A 1503 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8070 (mt) outliers start: 26 outliers final: 23 residues processed: 151 average time/residue: 0.2256 time to fit residues: 48.9523 Evaluate side-chains 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 73 optimal weight: 0.3980 chunk 64 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112782 restraints weight = 12967.872| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.81 r_work: 0.3058 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10708 Z= 0.140 Angle : 0.499 9.692 14519 Z= 0.253 Chirality : 0.038 0.169 1633 Planarity : 0.004 0.054 1779 Dihedral : 9.194 143.923 1543 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.59 % Allowed : 22.05 % Favored : 75.36 % 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: 1.20 (0.23), residues: 1242 helix: 1.91 (0.19), residues: 705 sheet: -0.42 (0.49), residues: 100 loop : -0.75 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.021 0.001 TYR A1509 ARG 0.002 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 583) hydrogen bonds : angle 4.02149 ( 1692) covalent geometry : bond 0.00330 (10708) covalent geometry : angle 0.49857 (14519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8924 (tttt) cc_final: 0.8544 (tptt) REVERT: A 1057 LEU cc_start: 0.8778 (mt) cc_final: 0.8307 (mp) REVERT: A 1271 MET cc_start: 0.7756 (tpt) cc_final: 0.7467 (tpt) REVERT: A 1304 MET cc_start: 0.7924 (mmt) cc_final: 0.7579 (mmm) REVERT: A 1451 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7455 (mm-40) REVERT: A 1503 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8118 (mt) outliers start: 29 outliers final: 26 residues processed: 148 average time/residue: 0.2263 time to fit residues: 47.9486 Evaluate side-chains 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113386 restraints weight = 12968.460| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.82 r_work: 0.3055 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10708 Z= 0.143 Angle : 0.504 13.013 14519 Z= 0.255 Chirality : 0.038 0.169 1633 Planarity : 0.004 0.054 1779 Dihedral : 9.190 143.948 1543 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.68 % Allowed : 22.05 % Favored : 75.27 % 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: 1.19 (0.23), residues: 1242 helix: 1.92 (0.19), residues: 702 sheet: -0.42 (0.49), residues: 100 loop : -0.76 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.007 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.021 0.001 TYR A1509 ARG 0.002 0.000 ARG A1238 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 583) hydrogen bonds : angle 4.02762 ( 1692) covalent geometry : bond 0.00338 (10708) covalent geometry : angle 0.50388 (14519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.23 seconds wall clock time: 96 minutes 50.76 seconds (5810.76 seconds total)