Starting phenix.real_space_refine on Wed Aug 5 17:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4t_16428/08_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_16428/08_2026/8c4t_16428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c4t_16428/08_2026/8c4t_16428.cif" } 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-2.2rc3-6140/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: {'RNAv2': 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: 2.29, per 1000 atoms: 0.22 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: 0.59 Conformation dependent library (CDL) restraints added in 235.8 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: 0.22 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: 1.43 Time building geometry restraints manager: 0.79 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=" O3' A C 5 " pdb=" P G C 6 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.66e+01 ... (remaining 10703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14279 1.95 - 3.89: 189 3.89 - 5.84: 35 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=" 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 angle pdb=" N GLN A1575 " pdb=" CA GLN A1575 " pdb=" C GLN A1575 " ideal model delta sigma weight residual 110.36 103.71 6.65 1.55e+00 4.16e-01 1.84e+01 ... (remaining 14514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5441 17.33 - 34.66: 716 34.66 - 51.99: 183 51.99 - 69.32: 41 69.32 - 86.65: 10 Dihedral angle restraints: 6391 sinusoidal: 2662 harmonic: 3729 Sorted by residual: dihedral pdb=" C4' G C 9 " pdb=" C3' G C 9 " pdb=" C2' G C 9 " pdb=" C1' G C 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.23 72.57 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' A C 12 " pdb=" C3' A C 12 " pdb=" C2' A C 12 " pdb=" C1' A C 12 " ideal model delta sinusoidal sigma weight residual 36.35 -35.03 71.38 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' A C 8 " pdb=" C3' A C 8 " pdb=" C2' A C 8 " pdb=" C1' A C 8 " ideal model delta sinusoidal sigma weight residual 36.34 -27.95 64.29 1 3.10e+00 1.04e-01 5.66e+02 ... (remaining 6388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1497 0.076 - 0.152: 109 0.152 - 0.228: 9 0.228 - 0.305: 14 0.305 - 0.381: 4 Chirality restraints: 1633 Sorted by residual: 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=" P G C 3 " pdb=" OP1 G C 3 " pdb=" OP2 G C 3 " pdb=" O5' G C 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" P G C 6 " pdb=" OP1 G C 6 " pdb=" OP2 G C 6 " pdb=" O5' G C 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.60e+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: 1.690 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- 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= 0.211 Angle : 0.595 9.729 14519 Z= 0.328 Chirality : 0.051 0.381 1633 Planarity : 0.004 0.046 1779 Dihedral : 16.701 86.645 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 0.00347 / 0.21 (10708) covalent geometry : angle 0.59519 / 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 : 0.245 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: 0.0927 time to fit residues: 17.7051 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 : 0.249 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.151600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114901 restraints weight = 12933.726| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.83 r_work: 0.3063 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0789 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= 0.137 Angle : 0.552 8.422 14519 Z= 0.275 Chirality : 0.042 0.356 1633 Planarity : 0.004 0.038 1779 Dihedral : 6.867 90.063 1514 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.59 % Allowed : 20.45 % 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: 1.05 (0.23), residues: 1242 helix: 1.73 (0.19), residues: 712 sheet: -0.40 (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 A 566 TYR 0.010 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 0.00313 / 0.14 (10708) covalent geometry : angle 0.55223 / 0.27 (14519) hydrogen bonds : bond 0.04120 / 2.60 ( 583) hydrogen bonds : angle 4.40448 / 3.22 ( 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7860 (t0) cc_final: 0.7617 (t0) REVERT: A 429 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 774 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8040 (mtt-85) REVERT: A 819 GLU cc_start: 0.7975 (mp0) cc_final: 0.7545 (mp0) outliers start: 29 outliers final: 15 residues processed: 156 average time/residue: 0.1037 time to fit residues: 23.1733 Evaluate side-chains 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.149045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112242 restraints weight = 13012.573| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.83 r_work: 0.3027 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10708 Z= 0.180 Angle : 0.538 9.974 14519 Z= 0.272 Chirality : 0.042 0.338 1633 Planarity : 0.004 0.041 1779 Dihedral : 7.027 109.094 1509 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.30 % Allowed : 20.09 % 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: 1.01 (0.23), residues: 1242 helix: 1.69 (0.19), residues: 710 sheet: -0.35 (0.51), residues: 99 loop : -0.76 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1427 TYR 0.015 0.002 TYR A 352 PHE 0.021 0.002 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (10708) covalent geometry : angle 0.53772 / 0.27 (14519) hydrogen bonds : bond 0.04346 / 2.76 ( 583) hydrogen bonds : angle 4.27803 / 3.13 ( 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 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8381 (t0) cc_final: 0.8175 (t0) REVERT: A 774 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8122 (mtt-85) REVERT: A 855 TYR cc_start: 0.8625 (t80) cc_final: 0.8328 (t80) REVERT: A 1305 LEU cc_start: 0.8633 (tp) cc_final: 0.8413 (tt) outliers start: 37 outliers final: 23 residues processed: 163 average time/residue: 0.0998 time to fit residues: 23.2025 Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 870 GLU 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 1030 MET 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 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: 2.9990 chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 87 optimal weight: 0.0010 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.150858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114403 restraints weight = 13041.012| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.80 r_work: 0.3071 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10708 Z= 0.134 Angle : 0.502 8.754 14519 Z= 0.253 Chirality : 0.040 0.315 1633 Planarity : 0.003 0.042 1779 Dihedral : 6.859 103.729 1509 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.68 % Allowed : 20.27 % Favored : 77.05 % 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: 1.19 (0.23), residues: 1242 helix: 1.85 (0.19), residues: 704 sheet: -0.30 (0.50), residues: 100 loop : -0.68 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.012 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 0.00314 / 0.13 (10708) covalent geometry : angle 0.50173 / 0.25 (14519) hydrogen bonds : bond 0.03798 / 2.40 ( 583) hydrogen bonds : angle 4.12560 / 3.01 ( 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 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8098 (t0) cc_final: 0.7890 (t0) REVERT: A 774 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8164 (mtt-85) REVERT: A 855 TYR cc_start: 0.8554 (t80) cc_final: 0.8166 (t80) REVERT: A 1057 LEU cc_start: 0.8789 (mt) cc_final: 0.8332 (mp) outliers start: 30 outliers final: 22 residues processed: 159 average time/residue: 0.0983 time to fit residues: 22.1302 Evaluate side-chains 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 545 THR 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 1030 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.147415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110720 restraints weight = 13109.722| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.82 r_work: 0.3029 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10708 Z= 0.216 Angle : 0.568 10.406 14519 Z= 0.285 Chirality : 0.043 0.329 1633 Planarity : 0.004 0.045 1779 Dihedral : 6.964 103.204 1509 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.20 % Allowed : 19.55 % 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: 0.91 (0.23), residues: 1242 helix: 1.60 (0.19), residues: 709 sheet: -0.37 (0.50), residues: 100 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1238 TYR 0.015 0.002 TYR A 352 PHE 0.023 0.002 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (10708) covalent geometry : angle 0.56848 / 0.29 (14519) hydrogen bonds : bond 0.04416 / 2.80 ( 583) hydrogen bonds : angle 4.25136 / 3.11 ( 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 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 926 TYR cc_start: 0.6927 (m-10) cc_final: 0.6679 (m-10) outliers start: 47 outliers final: 33 residues processed: 166 average time/residue: 0.0933 time to fit residues: 22.3040 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL 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 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 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 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 85 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115073 restraints weight = 13006.392| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.79 r_work: 0.3077 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1357 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= 0.117 Angle : 0.497 8.848 14519 Z= 0.251 Chirality : 0.040 0.303 1633 Planarity : 0.003 0.048 1779 Dihedral : 6.863 103.142 1509 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.68 % Allowed : 21.43 % Favored : 75.89 % 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: 1.20 (0.23), residues: 1242 helix: 1.89 (0.19), residues: 701 sheet: -0.35 (0.50), residues: 100 loop : -0.69 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.015 0.001 TYR A1509 PHE 0.017 0.001 PHE A1436 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10708) covalent geometry : angle 0.49659 / 0.25 (14519) hydrogen bonds : bond 0.03620 / 2.27 ( 583) hydrogen bonds : angle 4.07725 / 2.97 ( 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 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 735 MET cc_start: 0.9069 (tpp) cc_final: 0.8859 (tpp) REVERT: A 1057 LEU cc_start: 0.8774 (mt) cc_final: 0.8331 (mp) REVERT: A 1451 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 1511 PHE cc_start: 0.8544 (m-80) cc_final: 0.8222 (m-80) outliers start: 30 outliers final: 23 residues processed: 153 average time/residue: 0.0887 time to fit residues: 19.4852 Evaluate side-chains 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.149369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112802 restraints weight = 13013.493| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.81 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10708 Z= 0.156 Angle : 0.527 9.199 14519 Z= 0.263 Chirality : 0.041 0.309 1633 Planarity : 0.004 0.059 1779 Dihedral : 6.854 101.586 1509 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.04 % Allowed : 21.88 % Favored : 75.09 % 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: 1.13 (0.23), residues: 1242 helix: 1.83 (0.19), residues: 704 sheet: -0.41 (0.50), residues: 100 loop : -0.72 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.017 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 0.00369 / 0.16 (10708) covalent geometry : angle 0.52671 / 0.26 (14519) hydrogen bonds : bond 0.03881 / 2.44 ( 583) hydrogen bonds : angle 4.10688 / 2.99 ( 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 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 1057 LEU cc_start: 0.8794 (mt) cc_final: 0.8381 (mp) REVERT: A 1304 MET cc_start: 0.7917 (mmt) cc_final: 0.7562 (mmm) REVERT: A 1503 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 1511 PHE cc_start: 0.8556 (m-80) cc_final: 0.8233 (m-80) outliers start: 34 outliers final: 28 residues processed: 150 average time/residue: 0.0960 time to fit residues: 20.8150 Evaluate side-chains 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111375 restraints weight = 13051.218| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.79 r_work: 0.3035 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10708 Z= 0.190 Angle : 0.552 9.759 14519 Z= 0.276 Chirality : 0.042 0.315 1633 Planarity : 0.004 0.056 1779 Dihedral : 6.931 101.554 1509 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.39 % Allowed : 21.43 % Favored : 75.18 % 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: 1.00 (0.23), residues: 1242 helix: 1.72 (0.19), residues: 705 sheet: -0.44 (0.50), residues: 100 loop : -0.78 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.019 0.001 TYR A1509 PHE 0.021 0.002 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (10708) covalent geometry : angle 0.55206 / 0.28 (14519) hydrogen bonds : bond 0.04181 / 2.63 ( 583) hydrogen bonds : angle 4.18179 / 3.05 ( 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 165 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 735 MET cc_start: 0.9086 (tpp) cc_final: 0.8870 (tpp) REVERT: A 926 TYR cc_start: 0.6852 (m-10) cc_final: 0.6599 (m-10) REVERT: A 1304 MET cc_start: 0.7919 (mmt) cc_final: 0.7569 (mmm) REVERT: A 1451 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7437 (mm-40) outliers start: 38 outliers final: 31 residues processed: 156 average time/residue: 0.0924 time to fit residues: 20.7190 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114972 restraints weight = 12949.561| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.78 r_work: 0.3073 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1496 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= 0.126 Angle : 0.505 9.477 14519 Z= 0.253 Chirality : 0.040 0.295 1633 Planarity : 0.004 0.053 1779 Dihedral : 6.845 101.546 1509 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.21 % Allowed : 21.61 % Favored : 75.18 % 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: 1.16 (0.23), residues: 1242 helix: 1.87 (0.19), residues: 703 sheet: -0.39 (0.49), residues: 100 loop : -0.76 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.020 0.001 TYR A1509 PHE 0.019 0.001 PHE A1436 TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10708) covalent geometry : angle 0.50498 / 0.25 (14519) hydrogen bonds : bond 0.03603 / 2.26 ( 583) hydrogen bonds : angle 4.05633 / 2.95 ( 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 735 MET cc_start: 0.9019 (tpp) cc_final: 0.8788 (tpp) REVERT: A 855 TYR cc_start: 0.8613 (t80) cc_final: 0.8342 (t80) REVERT: A 1057 LEU cc_start: 0.8769 (mt) cc_final: 0.8320 (mp) REVERT: A 1304 MET cc_start: 0.7835 (mmt) cc_final: 0.7489 (mmm) REVERT: A 1451 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7427 (mm-40) REVERT: A 1503 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8039 (mt) outliers start: 36 outliers final: 31 residues processed: 154 average time/residue: 0.0913 time to fit residues: 20.3125 Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 970 SER 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 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 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 5 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108799 restraints weight = 13031.207| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.88 r_work: 0.2976 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 10708 Z= 0.344 Angle : 0.675 11.177 14519 Z= 0.339 Chirality : 0.048 0.341 1633 Planarity : 0.004 0.057 1779 Dihedral : 7.131 99.969 1509 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.30 % Allowed : 21.52 % Favored : 75.18 % 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: 0.54 (0.23), residues: 1242 helix: 1.32 (0.19), residues: 705 sheet: -0.55 (0.50), residues: 100 loop : -0.94 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1405 TYR 0.020 0.002 TYR A1509 PHE 0.030 0.002 PHE A 585 TRP 0.013 0.002 TRP A 473 HIS 0.011 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.34 (10708) covalent geometry : angle 0.67462 / 0.34 (14519) hydrogen bonds : bond 0.05178 / 3.29 ( 583) hydrogen bonds : angle 4.45807 / 3.25 ( 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 735 MET cc_start: 0.8980 (tpp) cc_final: 0.8753 (tpp) REVERT: A 855 TYR cc_start: 0.8629 (t80) cc_final: 0.8173 (t80) REVERT: A 1304 MET cc_start: 0.7921 (mmt) cc_final: 0.7585 (mmm) outliers start: 37 outliers final: 34 residues processed: 156 average time/residue: 0.0911 time to fit residues: 20.4603 Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 431 ILE Chi-restraints excluded: chain A residue 432 THR 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 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 970 SER 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 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 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 106 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112881 restraints weight = 12959.977| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.80 r_work: 0.3052 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1583 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= 0.144 Angle : 0.532 9.670 14519 Z= 0.268 Chirality : 0.041 0.302 1633 Planarity : 0.004 0.056 1779 Dihedral : 7.011 102.934 1509 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 21.79 % 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 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: 0.89 (0.23), residues: 1242 helix: 1.66 (0.19), residues: 705 sheet: -0.56 (0.50), residues: 100 loop : -0.89 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1238 TYR 0.021 0.001 TYR A1509 PHE 0.020 0.001 PHE A1436 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 0.00337 / 0.14 (10708) covalent geometry : angle 0.53240 / 0.27 (14519) hydrogen bonds : bond 0.03890 / 2.44 ( 583) hydrogen bonds : angle 4.19099 / 3.05 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.07 seconds wall clock time: 42 minutes 59.81 seconds (2579.81 seconds total)