Starting phenix.real_space_refine on Thu Jul 2 23:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4t_16428/07_2026/8c4t_16428.map" } resolution = 3.23 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.84, per 1000 atoms: 0.18 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: 0.60 Conformation dependent library (CDL) restraints added in 253.5 milliseconds 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: 0.29 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: 1.51 Time building geometry restraints manager: 0.83 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: 6035 29.13 - 58.25: 335 58.25 - 87.37: 19 87.37 - 116.50: 1 116.50 - 145.62: 1 Dihedral angle restraints: 6391 sinusoidal: 2662 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 6388 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: 1.040 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 16.492 145.624 3971 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 566 TYR 0.010 0.001 TYR A1306 PHE 0.014 0.001 PHE A 585 TRP 0.018 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.21 (10708) covalent geometry : angle 0.58027 / 0.33 (14519) hydrogen bonds : bond 0.14139 / 9.19 ( 583) hydrogen bonds : angle 5.82339 / 4.18 ( 1692) *********************** 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 : 0.320 Fit side-chains REVERT: A 575 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: A 735 MET cc_start: 0.9024 (tpp) cc_final: 0.8823 (tpp) 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: 0.0918 time to fit residues: 17.2706 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 : 0.286 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 HIS A 858 ASN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114912 restraints weight = 12975.635| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.81 r_work: 0.3055 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10708 Z= 0.136 Angle : 0.493 8.377 14519 Z= 0.257 Chirality : 0.038 0.180 1633 Planarity : 0.004 0.038 1779 Dihedral : 7.266 143.984 1514 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.14 % Allowed : 20.89 % Favored : 76.96 % 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 are not related in a simple way. whole: 1.06 (0.24), residues: 1242 helix: 1.73 (0.19), residues: 712 sheet: -0.41 (0.50), residues: 95 loop : -0.75 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1427 TYR 0.009 0.001 TYR A 352 PHE 0.016 0.001 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10708) covalent geometry : angle 0.49275 / 0.26 (14519) hydrogen bonds : bond 0.04383 / 2.77 ( 583) hydrogen bonds : angle 4.47237 / 3.27 ( 1692) *********************** 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 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7850 (t0) cc_final: 0.7574 (t0) REVERT: A 429 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8512 (tt) REVERT: A 458 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7572 (mp0) REVERT: A 774 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8089 (mtt-85) REVERT: A 819 GLU cc_start: 0.7966 (mp0) cc_final: 0.7525 (mp0) outliers start: 24 outliers final: 13 residues processed: 152 average time/residue: 0.0848 time to fit residues: 18.5413 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 520 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 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 1527 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 GLN A1434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115266 restraints weight = 13034.010| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.79 r_work: 0.3070 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0953 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= 0.122 Angle : 0.464 8.153 14519 Z= 0.241 Chirality : 0.037 0.189 1633 Planarity : 0.003 0.041 1779 Dihedral : 6.886 143.833 1509 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.12 % Allowed : 20.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1242 helix: 1.89 (0.19), residues: 706 sheet: -0.33 (0.51), residues: 99 loop : -0.70 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1427 TYR 0.015 0.001 TYR A1253 PHE 0.016 0.001 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10708) covalent geometry : angle 0.46420 / 0.24 (14519) hydrogen bonds : bond 0.03811 / 2.41 ( 583) hydrogen bonds : angle 4.18353 / 3.05 ( 1692) *********************** 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 172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 429 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 774 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8171 (mtt-85) REVERT: A 819 GLU cc_start: 0.7957 (mp0) cc_final: 0.7543 (mp0) REVERT: A 1305 LEU cc_start: 0.8581 (tp) cc_final: 0.8372 (tt) outliers start: 35 outliers final: 20 residues processed: 163 average time/residue: 0.0850 time to fit residues: 19.7898 Evaluate side-chains 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 429 LEU 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 805 SER 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 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 88 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3752 r_free = 0.3752 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114288 restraints weight = 13078.967| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.80 r_work: 0.3057 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1122 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= 0.136 Angle : 0.472 8.445 14519 Z= 0.245 Chirality : 0.037 0.147 1633 Planarity : 0.003 0.045 1779 Dihedral : 6.825 143.510 1509 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.12 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1242 helix: 1.91 (0.19), residues: 704 sheet: -0.27 (0.51), residues: 100 loop : -0.64 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.013 0.001 TYR A1253 PHE 0.017 0.001 PHE A 585 TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10708) covalent geometry : angle 0.47244 / 0.24 (14519) hydrogen bonds : bond 0.03796 / 2.39 ( 583) hydrogen bonds : angle 4.08871 / 2.98 ( 1692) *********************** 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 165 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8034 (t0) cc_final: 0.7821 (t0) REVERT: A 429 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 774 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8052 (mtt-85) REVERT: A 1305 LEU cc_start: 0.8636 (tp) cc_final: 0.8428 (tt) outliers start: 35 outliers final: 27 residues processed: 157 average time/residue: 0.0810 time to fit residues: 18.2847 Evaluate side-chains 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 429 LEU 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 805 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 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL 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 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 32 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3742 r_free = 0.3742 target = 0.149725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113440 restraints weight = 13094.142| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.83 r_work: 0.3032 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10708 Z= 0.142 Angle : 0.478 8.900 14519 Z= 0.247 Chirality : 0.037 0.142 1633 Planarity : 0.003 0.049 1779 Dihedral : 6.781 143.366 1509 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.66 % Allowed : 20.18 % Favored : 76.16 % 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 are not related in a simple way. whole: 1.23 (0.23), residues: 1242 helix: 1.89 (0.19), residues: 704 sheet: -0.32 (0.50), residues: 100 loop : -0.65 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.015 0.001 TYR A1509 PHE 0.018 0.001 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10708) covalent geometry : angle 0.47757 / 0.25 (14519) hydrogen bonds : bond 0.03806 / 2.40 ( 583) hydrogen bonds : angle 4.04754 / 2.95 ( 1692) *********************** 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 171 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8004 (t0) cc_final: 0.7794 (t0) REVERT: A 461 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8474 (tptt) REVERT: A 774 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8111 (mtt-85) REVERT: A 1057 LEU cc_start: 0.8739 (mt) cc_final: 0.8222 (mp) REVERT: A 1305 LEU cc_start: 0.8628 (tp) cc_final: 0.8422 (tt) outliers start: 41 outliers final: 29 residues processed: 164 average time/residue: 0.0960 time to fit residues: 22.2751 Evaluate side-chains 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 805 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 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL 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 85 optimal weight: 0.4980 chunk 120 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3754 r_free = 0.3754 target = 0.150750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114128 restraints weight = 13043.267| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.83 r_work: 0.3077 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1322 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= 0.116 Angle : 0.461 8.996 14519 Z= 0.238 Chirality : 0.036 0.141 1633 Planarity : 0.003 0.052 1779 Dihedral : 6.683 144.362 1509 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.04 % Allowed : 20.80 % Favored : 76.16 % 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 are not related in a simple way. whole: 1.32 (0.23), residues: 1242 helix: 1.98 (0.19), residues: 701 sheet: -0.32 (0.50), residues: 100 loop : -0.61 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.016 0.001 TYR A1509 PHE 0.016 0.001 PHE A 585 TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10708) covalent geometry : angle 0.46081 / 0.24 (14519) hydrogen bonds : bond 0.03529 / 2.22 ( 583) hydrogen bonds : angle 3.99558 / 2.90 ( 1692) *********************** 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 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8499 (tptt) REVERT: A 774 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8165 (mtt-85) REVERT: A 819 GLU cc_start: 0.8064 (mp0) cc_final: 0.7659 (mp0) REVERT: A 1304 MET cc_start: 0.7889 (mmt) cc_final: 0.7530 (mmm) REVERT: A 1305 LEU cc_start: 0.8684 (tp) cc_final: 0.8471 (tt) REVERT: A 1451 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7473 (mm-40) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.0919 time to fit residues: 20.6861 Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 805 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 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 1380 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 13 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 0.0010 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3753 r_free = 0.3753 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114049 restraints weight = 12968.623| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.81 r_work: 0.3073 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10708 Z= 0.127 Angle : 0.471 9.312 14519 Z= 0.243 Chirality : 0.037 0.159 1633 Planarity : 0.003 0.053 1779 Dihedral : 6.648 144.468 1509 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1242 helix: 1.97 (0.19), residues: 701 sheet: -0.31 (0.50), residues: 100 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.017 0.001 TYR A1509 PHE 0.017 0.001 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10708) covalent geometry : angle 0.47148 / 0.24 (14519) hydrogen bonds : bond 0.03606 / 2.26 ( 583) hydrogen bonds : angle 4.00121 / 2.91 ( 1692) *********************** 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8508 (tptt) REVERT: A 1304 MET cc_start: 0.7905 (mmt) cc_final: 0.7541 (mmm) REVERT: A 1305 LEU cc_start: 0.8744 (tp) cc_final: 0.8531 (tt) outliers start: 32 outliers final: 26 residues processed: 157 average time/residue: 0.0861 time to fit residues: 19.6414 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR 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 805 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 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 1471 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 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 109 optimal weight: 0.0050 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3735 r_free = 0.3735 target = 0.149067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112814 restraints weight = 13050.175| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.80 r_work: 0.3061 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10708 Z= 0.157 Angle : 0.495 9.516 14519 Z= 0.254 Chirality : 0.038 0.170 1633 Planarity : 0.004 0.061 1779 Dihedral : 6.686 143.660 1509 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.95 % Allowed : 20.89 % Favored : 76.16 % 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 are not related in a simple way. whole: 1.22 (0.23), residues: 1242 helix: 1.90 (0.19), residues: 703 sheet: -0.36 (0.50), residues: 100 loop : -0.68 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.018 0.001 TYR A1509 PHE 0.018 0.001 PHE A 585 TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10708) covalent geometry : angle 0.49544 / 0.25 (14519) hydrogen bonds : bond 0.03870 / 2.43 ( 583) hydrogen bonds : angle 4.05808 / 2.95 ( 1692) *********************** 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 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8511 (tptt) REVERT: A 819 GLU cc_start: 0.8004 (mp0) cc_final: 0.7606 (mp0) REVERT: A 1304 MET cc_start: 0.7886 (mmt) cc_final: 0.7520 (mmm) REVERT: A 1305 LEU cc_start: 0.8733 (tp) cc_final: 0.8531 (tt) outliers start: 33 outliers final: 29 residues processed: 151 average time/residue: 0.0800 time to fit residues: 17.6605 Evaluate side-chains 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR 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 805 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.0170 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3787 r_free = 0.3787 target = 0.153502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117418 restraints weight = 12937.263| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.81 r_work: 0.3113 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10708 Z= 0.091 Angle : 0.453 9.222 14519 Z= 0.232 Chirality : 0.036 0.147 1633 Planarity : 0.003 0.054 1779 Dihedral : 6.520 146.506 1509 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.79 % Allowed : 22.14 % Favored : 76.07 % 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 are not related in a simple way. whole: 1.43 (0.24), residues: 1242 helix: 2.10 (0.19), residues: 703 sheet: -0.34 (0.50), residues: 98 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.020 0.001 TYR A1509 PHE 0.014 0.001 PHE A1450 TRP 0.017 0.001 TRP A 473 HIS 0.003 0.000 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10708) covalent geometry : angle 0.45312 / 0.23 (14519) hydrogen bonds : bond 0.03163 / 1.98 ( 583) hydrogen bonds : angle 3.89687 / 2.82 ( 1692) *********************** 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 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 461 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8492 (tptt) REVERT: A 774 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8113 (mtt-85) REVERT: A 1304 MET cc_start: 0.7851 (mmt) cc_final: 0.7507 (mmm) REVERT: A 1305 LEU cc_start: 0.8768 (tp) cc_final: 0.8565 (tt) outliers start: 20 outliers final: 19 residues processed: 148 average time/residue: 0.0907 time to fit residues: 19.3965 Evaluate side-chains 145 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1281 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 1464 TRP 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 5 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3687 r_free = 0.3687 target = 0.144899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108555 restraints weight = 13076.805| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.90 r_work: 0.3003 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10708 Z= 0.272 Angle : 0.592 9.661 14519 Z= 0.303 Chirality : 0.042 0.158 1633 Planarity : 0.004 0.056 1779 Dihedral : 6.843 141.243 1509 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.88 % Allowed : 21.88 % Favored : 76.25 % 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 are not related in a simple way. whole: 0.95 (0.23), residues: 1242 helix: 1.66 (0.19), residues: 704 sheet: -0.44 (0.50), residues: 100 loop : -0.79 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1238 TYR 0.020 0.002 TYR A1509 PHE 0.027 0.002 PHE A 585 TRP 0.014 0.002 TRP A 473 HIS 0.005 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.27 (10708) covalent geometry : angle 0.59239 / 0.30 (14519) hydrogen bonds : bond 0.04686 / 2.97 ( 583) hydrogen bonds : angle 4.25731 / 3.10 ( 1692) ********************** 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 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 926 TYR cc_start: 0.6775 (m-10) cc_final: 0.6524 (m-10) REVERT: A 1304 MET cc_start: 0.7875 (mmt) cc_final: 0.7516 (mmm) REVERT: A 1488 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6792 (mmt180) outliers start: 21 outliers final: 21 residues processed: 143 average time/residue: 0.0838 time to fit residues: 17.0600 Evaluate side-chains 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR 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 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 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1281 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 1464 TRP 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 106 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3736 r_free = 0.3736 target = 0.149146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113104 restraints weight = 13046.989| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.81 r_work: 0.3043 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10708 Z= 0.146 Angle : 0.503 9.705 14519 Z= 0.258 Chirality : 0.038 0.146 1633 Planarity : 0.004 0.055 1779 Dihedral : 6.711 142.628 1509 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.14 % Allowed : 21.79 % Favored : 76.07 % 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 are not related in a simple way. whole: 1.10 (0.23), residues: 1242 helix: 1.84 (0.19), residues: 699 sheet: -0.46 (0.50), residues: 100 loop : -0.76 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.021 0.001 TYR A1509 PHE 0.019 0.001 PHE A1436 TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10708) covalent geometry : angle 0.50263 / 0.26 (14519) hydrogen bonds : bond 0.03841 / 2.41 ( 583) hydrogen bonds : angle 4.09253 / 2.97 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.60 seconds wall clock time: 39 minutes 29.69 seconds (2369.69 seconds total)