Starting phenix.real_space_refine on Fri Oct 23 20:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.cif Found real_map, /net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.map" model { file = "/net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26kd_80710/10_2026/26kd_80710.cif" } resolution = 2.64 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= 0.013 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 Mg 1 5.21 5 S 79 5.16 5 C 6741 2.51 5 N 1830 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10638 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10634 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 41, 'TRANS': 1316} Chain breaks: 12 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 116 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' MN': 1, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 796 SG CYS A1028 25.743 17.493 91.975 1.00 98.27 S ATOM 815 SG CYS A1031 28.785 15.262 91.651 1.00 96.14 S ATOM 1054 SG CYS A1062 25.450 14.003 90.345 1.00114.33 S ATOM 1074 SG CYS A1065 27.191 16.870 88.571 1.00111.87 S ATOM 1591 SG CYS A1294 38.747 26.092 40.886 1.00 72.29 S Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10638 At special positions: 0 Unit cell: (95.63, 106.58, 121.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 79 16.00 Mg 1 11.99 O 1984 8.00 N 1830 7.00 C 6741 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: 0.90 Conformation dependent library (CDL) restraints added in 371.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " Number of angles added : 6 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2606 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 63.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 5.330A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.930A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 removed outlier: 3.708A pdb=" N THR A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1056 Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1266 through 1279 removed outlier: 4.153A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1282 No H-bonds generated for 'chain 'A' and resid 1280 through 1282' Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.654A pdb=" N ILE A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 Processing helix chain 'A' and resid 1315 through 1329 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 4.217A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1435 removed outlier: 3.941A pdb=" N VAL A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 Processing helix chain 'A' and resid 1465 through 1481 Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.672A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1531 removed outlier: 4.128A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A1527 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1538 through 1547 removed outlier: 3.725A pdb=" N SER A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1570 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.873A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 Processing helix chain 'A' and resid 1613 through 1616 Processing helix chain 'A' and resid 1631 through 1651 Processing helix chain 'A' and resid 1659 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1792 Processing helix chain 'A' and resid 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 2295 through 2307 removed outlier: 3.850A pdb=" N THR A2306 " --> pdb=" O ASN A2302 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2397 Processing helix chain 'A' and resid 2448 through 2457 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.789A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2559 removed outlier: 4.816A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.508A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.522A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2595 through 2600' Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.559A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.534A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.692A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 Processing helix chain 'A' and resid 2698 through 2701 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2816 through 2836 Processing helix chain 'A' and resid 2899 through 2911 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3072 Processing helix chain 'A' and resid 3093 through 3099 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3114 through 3122 removed outlier: 4.216A pdb=" N ILE A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3127 through 3129 No H-bonds generated for 'chain 'A' and resid 3127 through 3129' Processing helix chain 'A' and resid 3130 through 3141 removed outlier: 3.602A pdb=" N GLN A3140 " --> pdb=" O PHE A3136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A3141 " --> pdb=" O LYS A3137 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3172 Processing helix chain 'A' and resid 3174 through 3185 Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.749A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972 removed outlier: 6.715A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 3.830A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A1382 " --> pdb=" O PHE A1398 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A1398 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS A1384 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY A1396 " --> pdb=" O CYS A1384 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A1386 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2507 through 2514 removed outlier: 3.536A pdb=" N TYR A2519 " --> pdb=" O GLY A2357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2400 through 2402 Processing sheet with id=AA6, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.593A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.712A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3079 through 3080 Processing sheet with id=AA9, first strand: chain 'A' and resid 3086 through 3089 629 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3474 1.34 - 1.46: 2378 1.46 - 1.58: 4855 1.58 - 1.69: 0 1.69 - 1.81: 113 Bond restraints: 10820 Sorted by residual: bond pdb=" CG PRO A3022 " pdb=" CD PRO A3022 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.64e+00 bond pdb=" CB PRO A3022 " pdb=" CG PRO A3022 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.34e+00 bond pdb=" CB ASP A2309 " pdb=" CG ASP A2309 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB THR A1345 " pdb=" CG2 THR A1345 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CG ARG A1638 " pdb=" CD ARG A1638 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 14450 1.71 - 3.42: 157 3.42 - 5.13: 15 5.13 - 6.83: 7 6.83 - 8.54: 4 Bond angle restraints: 14633 Sorted by residual: angle pdb=" CA PRO A3022 " pdb=" N PRO A3022 " pdb=" CD PRO A3022 " ideal model delta sigma weight residual 112.00 108.13 3.87 1.40e+00 5.10e-01 7.66e+00 angle pdb=" CB MET A1792 " pdb=" CG MET A1792 " pdb=" SD MET A1792 " ideal model delta sigma weight residual 112.70 120.30 -7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" CA LEU A1052 " pdb=" CB LEU A1052 " pdb=" CG LEU A1052 " ideal model delta sigma weight residual 116.30 124.84 -8.54 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CG ARG A1638 " pdb=" CD ARG A1638 " pdb=" NE ARG A1638 " ideal model delta sigma weight residual 112.00 117.23 -5.23 2.20e+00 2.07e-01 5.65e+00 angle pdb=" CB MET A2375 " pdb=" CG MET A2375 " pdb=" SD MET A2375 " ideal model delta sigma weight residual 112.70 119.40 -6.70 3.00e+00 1.11e-01 4.99e+00 ... (remaining 14628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5632 17.97 - 35.95: 719 35.95 - 53.92: 178 53.92 - 71.90: 26 71.90 - 89.87: 16 Dihedral angle restraints: 6571 sinusoidal: 2580 harmonic: 3991 Sorted by residual: dihedral pdb=" CA ASN A3201 " pdb=" C ASN A3201 " pdb=" N LEU A3202 " pdb=" CA LEU A3202 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB GLU A1086 " pdb=" CG GLU A1086 " pdb=" CD GLU A1086 " pdb=" OE1 GLU A1086 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 996 " pdb=" CG GLU A 996 " pdb=" CD GLU A 996 " pdb=" OE1 GLU A 996 " ideal model delta sinusoidal sigma weight residual 0.00 -88.58 88.58 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1209 0.033 - 0.066: 359 0.066 - 0.099: 96 0.099 - 0.133: 38 0.133 - 0.166: 5 Chirality restraints: 1707 Sorted by residual: chirality pdb=" CB VAL A1570 " pdb=" CA VAL A1570 " pdb=" CG1 VAL A1570 " pdb=" CG2 VAL A1570 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CG LEU A1052 " pdb=" CB LEU A1052 " pdb=" CD1 LEU A1052 " pdb=" CD2 LEU A1052 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE A2353 " pdb=" N ILE A2353 " pdb=" C ILE A2353 " pdb=" CB ILE A2353 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1704 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A3021 " -0.066 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO A3022 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A3022 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A3022 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 948 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 949 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 949 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 949 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1638 " -0.104 9.50e-02 1.11e+02 4.73e-02 2.18e+00 pdb=" NE ARG A1638 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1638 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A1638 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A1638 " 0.001 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 138 2.62 - 3.19: 9453 3.19 - 3.76: 17680 3.76 - 4.33: 23707 4.33 - 4.90: 39457 Nonbonded interactions: 90435 Sorted by model distance: nonbonded pdb=" OE2 GLU A3081 " pdb="MG MG A4004 " model vdw 2.050 2.170 nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.082 2.230 nonbonded pdb=" OE1 GLU A2575 " pdb="MN MN A4003 " model vdw 2.136 2.320 nonbonded pdb=" OD2 ASP A2518 " pdb="MN MN A4003 " model vdw 2.161 2.320 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.165 2.320 ... (remaining 90430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.002 0.058 10826 Z= 0.095 Angle : 0.469 8.542 14639 Z= 0.248 Chirality : 0.037 0.166 1707 Planarity : 0.004 0.099 1858 Dihedral : 17.196 89.869 3965 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.08 % Allowed : 25.13 % Favored : 74.79 % 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: 1.91 (0.24), residues: 1332 helix: 2.41 (0.19), residues: 786 sheet: 1.09 (0.65), residues: 72 loop : -0.71 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1638 TYR 0.025 0.001 TYR A1054 PHE 0.014 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (10820) covalent geometry : angle 0.46817 / 0.25 (14633) hydrogen bonds : bond 0.10510 / 7.14 ( 629) hydrogen bonds : angle 4.43207 / 3.15 ( 1821) metal coordination : bond 0.00147 / 0.09 ( 6) metal coordination : angle 1.44779 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 2996 HIS cc_start: 0.7984 (t-90) cc_final: 0.7525 (t70) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.4897 time to fit residues: 66.6678 Evaluate side-chains 110 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 ASN A1401 ASN A1404 GLN A1613 ASN A2376 GLN A2702 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092669 restraints weight = 16114.247| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.63 r_work: 0.3067 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10826 Z= 0.200 Angle : 0.533 9.295 14639 Z= 0.277 Chirality : 0.041 0.164 1707 Planarity : 0.004 0.067 1858 Dihedral : 3.745 21.616 1453 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.36 % Allowed : 24.20 % Favored : 72.44 % 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: 1.62 (0.23), residues: 1332 helix: 2.13 (0.18), residues: 795 sheet: 0.84 (0.63), residues: 72 loop : -0.77 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1638 TYR 0.019 0.001 TYR A1503 PHE 0.024 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (10820) covalent geometry : angle 0.53158 / 0.28 (14633) hydrogen bonds : bond 0.03904 / 2.61 ( 629) hydrogen bonds : angle 4.02464 / 2.82 ( 1821) metal coordination : bond 0.00334 / 0.19 ( 6) metal coordination : angle 2.20790 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7645 (ttt90) REVERT: A 1021 GLU cc_start: 0.8184 (tp30) cc_final: 0.7705 (tp30) REVERT: A 1364 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7926 (mtt-85) REVERT: A 1449 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 1465 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7446 (mpt90) REVERT: A 1647 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7676 (mtp) REVERT: A 2365 ILE cc_start: 0.8770 (mp) cc_final: 0.8231 (mm) REVERT: A 2996 HIS cc_start: 0.8316 (t-90) cc_final: 0.7760 (t70) REVERT: A 3109 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6001 (mtm) REVERT: A 3211 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7524 (mp0) outliers start: 40 outliers final: 18 residues processed: 147 average time/residue: 0.4608 time to fit residues: 74.2734 Evaluate side-chains 130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2699 VAL Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3109 MET Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [74, 86, 0, 93, 31, 96, 90, 127, 122, 39, 40] chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 ASN A1401 ASN A1799 ASN A2302 ASN A2560 GLN A2702 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093552 restraints weight = 16270.397| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.64 r_work: 0.3080 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10826 Z= 0.148 Angle : 0.502 8.371 14639 Z= 0.260 Chirality : 0.039 0.158 1707 Planarity : 0.003 0.058 1858 Dihedral : 3.724 20.150 1453 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.45 % Allowed : 24.62 % Favored : 71.93 % 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: 1.55 (0.23), residues: 1332 helix: 2.13 (0.18), residues: 794 sheet: 0.76 (0.63), residues: 72 loop : -0.91 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1638 TYR 0.012 0.001 TYR A1503 PHE 0.021 0.001 PHE A2633 TRP 0.017 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10820) covalent geometry : angle 0.50051 / 0.26 (14633) hydrogen bonds : bond 0.03579 / 2.40 ( 629) hydrogen bonds : angle 3.92430 / 2.74 ( 1821) metal coordination : bond 0.00307 / 0.19 ( 6) metal coordination : angle 2.01557 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7613 (ttt90) REVERT: A 1021 GLU cc_start: 0.8174 (tp30) cc_final: 0.7622 (tp30) REVERT: A 1364 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7928 (mtt-85) REVERT: A 1449 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 1647 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: A 2365 ILE cc_start: 0.8723 (mp) cc_final: 0.8436 (mm) REVERT: A 2579 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 2996 HIS cc_start: 0.8300 (t-90) cc_final: 0.7734 (t70) outliers start: 41 outliers final: 23 residues processed: 145 average time/residue: 0.4742 time to fit residues: 75.6073 Evaluate side-chains 137 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2699 VAL Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [0, 91, 72, 52, 41, 5, 47, 77, 67, 40, 106] chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.0050 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 ASN A1401 ASN A1768 GLN A2702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094912 restraints weight = 16186.726| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.65 r_work: 0.3104 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10826 Z= 0.114 Angle : 0.480 7.864 14639 Z= 0.250 Chirality : 0.038 0.145 1707 Planarity : 0.003 0.056 1858 Dihedral : 3.657 19.540 1453 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.61 % Allowed : 24.54 % Favored : 71.85 % 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: 1.63 (0.23), residues: 1332 helix: 2.19 (0.18), residues: 794 sheet: 0.82 (0.64), residues: 72 loop : -0.88 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1638 TYR 0.017 0.001 TYR A1054 PHE 0.018 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10820) covalent geometry : angle 0.47828 / 0.25 (14633) hydrogen bonds : bond 0.03311 / 2.21 ( 629) hydrogen bonds : angle 3.81291 / 2.67 ( 1821) metal coordination : bond 0.00241 / 0.15 ( 6) metal coordination : angle 2.20435 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7569 (ttt90) REVERT: A 1021 GLU cc_start: 0.8188 (tp30) cc_final: 0.7673 (tp30) REVERT: A 1364 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7895 (mtt-85) REVERT: A 1449 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 1647 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7670 (mtp) REVERT: A 2298 MET cc_start: 0.8183 (ttp) cc_final: 0.7967 (ttp) REVERT: A 2579 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 2996 HIS cc_start: 0.8281 (t-90) cc_final: 0.7693 (t70) REVERT: A 3139 MET cc_start: 0.7596 (ttm) cc_final: 0.7336 (tpt) REVERT: A 3224 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (mtm-85) outliers start: 43 outliers final: 20 residues processed: 149 average time/residue: 0.4679 time to fit residues: 76.5448 Evaluate side-chains 131 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2699 VAL Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [56, 87, 91, 41, 88, 28, 90, 14, 61, 106, 9] chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 ASN A1401 ASN A1768 GLN A1799 ASN A2302 ASN A2381 ASN A2702 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092206 restraints weight = 16164.158| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.64 r_work: 0.3061 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10826 Z= 0.180 Angle : 0.522 8.984 14639 Z= 0.270 Chirality : 0.040 0.189 1707 Planarity : 0.004 0.053 1858 Dihedral : 3.777 19.418 1453 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.87 % Allowed : 24.62 % Favored : 71.51 % 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: 1.48 (0.23), residues: 1332 helix: 2.08 (0.18), residues: 794 sheet: 0.61 (0.64), residues: 72 loop : -0.94 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1638 TYR 0.014 0.001 TYR A1503 PHE 0.024 0.001 PHE A2633 TRP 0.017 0.001 TRP A2542 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (10820) covalent geometry : angle 0.52046 / 0.27 (14633) hydrogen bonds : bond 0.03607 / 2.43 ( 629) hydrogen bonds : angle 3.94278 / 2.75 ( 1821) metal coordination : bond 0.00389 / 0.24 ( 6) metal coordination : angle 2.12174 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7617 (ttt90) REVERT: A 1021 GLU cc_start: 0.8204 (tp30) cc_final: 0.7621 (tp30) REVERT: A 1364 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7919 (mtt-85) REVERT: A 1449 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 1647 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: A 2579 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 2996 HIS cc_start: 0.8301 (t-90) cc_final: 0.7704 (t70) REVERT: A 3109 MET cc_start: 0.6357 (mpp) cc_final: 0.5887 (mtm) REVERT: A 3139 MET cc_start: 0.7672 (ttm) cc_final: 0.7396 (tpt) REVERT: A 3224 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7843 (mtm-85) outliers start: 46 outliers final: 26 residues processed: 147 average time/residue: 0.4617 time to fit residues: 74.5480 Evaluate side-chains 142 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2699 VAL Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [103, 81, 10, 1, 72, 102, 119, 15, 117, 91, 125] chunk 103 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 ASN A1401 ASN A1768 GLN A1799 ASN A2702 GLN A2776 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093190 restraints weight = 16161.258| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.63 r_work: 0.3077 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10826 Z= 0.141 Angle : 0.506 8.925 14639 Z= 0.260 Chirality : 0.039 0.158 1707 Planarity : 0.003 0.052 1858 Dihedral : 3.751 19.093 1453 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.87 % Allowed : 24.45 % Favored : 71.68 % 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: 1.56 (0.23), residues: 1332 helix: 2.15 (0.18), residues: 794 sheet: 0.71 (0.64), residues: 72 loop : -0.93 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1638 TYR 0.018 0.001 TYR A1054 PHE 0.022 0.001 PHE A2633 TRP 0.017 0.001 TRP A2542 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10820) covalent geometry : angle 0.50460 / 0.26 (14633) hydrogen bonds : bond 0.03432 / 2.29 ( 629) hydrogen bonds : angle 3.86567 / 2.70 ( 1821) metal coordination : bond 0.00297 / 0.19 ( 6) metal coordination : angle 2.21310 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 941 MET cc_start: 0.8846 (mtm) cc_final: 0.8596 (mtm) REVERT: A 990 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7601 (ttt90) REVERT: A 1021 GLU cc_start: 0.8186 (tp30) cc_final: 0.7572 (tp30) REVERT: A 1364 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7971 (mtt-85) REVERT: A 1449 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 2579 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 2996 HIS cc_start: 0.8281 (t-90) cc_final: 0.7657 (t70) REVERT: A 3109 MET cc_start: 0.6368 (mpp) cc_final: 0.5916 (mtm) REVERT: A 3139 MET cc_start: 0.7662 (ttm) cc_final: 0.7400 (tpt) REVERT: A 3203 MET cc_start: 0.6106 (pmm) cc_final: 0.5421 (pmm) REVERT: A 3224 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7831 (mtm-85) outliers start: 46 outliers final: 27 residues processed: 151 average time/residue: 0.4488 time to fit residues: 74.8243 Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2450 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [77, 96, 95, 8, 6, 114, 59, 47, 78, 102, 104] chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 104 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1401 ASN A1768 GLN A1799 ASN A2302 ASN A2702 GLN A2776 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093967 restraints weight = 16133.387| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.62 r_work: 0.3087 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10826 Z= 0.128 Angle : 0.511 8.824 14639 Z= 0.260 Chirality : 0.039 0.158 1707 Planarity : 0.003 0.052 1858 Dihedral : 3.709 17.775 1453 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.45 % Allowed : 24.87 % Favored : 71.68 % 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: 1.58 (0.23), residues: 1332 helix: 2.16 (0.18), residues: 794 sheet: 0.75 (0.64), residues: 72 loop : -0.91 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1638 TYR 0.010 0.001 TYR A1503 PHE 0.021 0.001 PHE A2633 TRP 0.017 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10820) covalent geometry : angle 0.50934 / 0.26 (14633) hydrogen bonds : bond 0.03348 / 2.24 ( 629) hydrogen bonds : angle 3.83834 / 2.68 ( 1821) metal coordination : bond 0.00285 / 0.18 ( 6) metal coordination : angle 2.20385 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7588 (ttt90) REVERT: A 1021 GLU cc_start: 0.8153 (tp30) cc_final: 0.7539 (tp30) REVERT: A 1364 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7900 (mtt-85) REVERT: A 1449 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 2579 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 2996 HIS cc_start: 0.8255 (t-90) cc_final: 0.7621 (t70) REVERT: A 3109 MET cc_start: 0.6375 (mpp) cc_final: 0.5894 (mtm) REVERT: A 3139 MET cc_start: 0.7671 (ttm) cc_final: 0.7386 (tpt) REVERT: A 3224 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7844 (mtm-85) outliers start: 41 outliers final: 31 residues processed: 146 average time/residue: 0.4198 time to fit residues: 67.8751 Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2450 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [75, 48, 133, 76, 100, 58, 46, 127, 16, 34, 20] chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1401 ASN A1768 GLN A1799 ASN A2702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090918 restraints weight = 16012.468| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.59 r_work: 0.3040 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10826 Z= 0.233 Angle : 0.587 12.424 14639 Z= 0.296 Chirality : 0.042 0.176 1707 Planarity : 0.004 0.051 1858 Dihedral : 3.879 19.881 1453 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.61 % Allowed : 25.21 % Favored : 71.18 % 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: 1.37 (0.23), residues: 1332 helix: 2.00 (0.18), residues: 794 sheet: 0.47 (0.64), residues: 72 loop : -0.96 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1638 TYR 0.017 0.001 TYR A1503 PHE 0.028 0.002 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (10820) covalent geometry : angle 0.58595 / 0.30 (14633) hydrogen bonds : bond 0.03868 / 2.58 ( 629) hydrogen bonds : angle 4.05987 / 2.83 ( 1821) metal coordination : bond 0.00533 / 0.32 ( 6) metal coordination : angle 2.03286 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7645 (ttt90) REVERT: A 1021 GLU cc_start: 0.8194 (tp30) cc_final: 0.7556 (tp30) REVERT: A 1364 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7996 (mtt-85) REVERT: A 1449 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8293 (p) REVERT: A 1478 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8315 (pmm-80) REVERT: A 2579 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 2996 HIS cc_start: 0.8291 (t-90) cc_final: 0.7693 (t70) REVERT: A 3109 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.5876 (mtm) REVERT: A 3139 MET cc_start: 0.7701 (ttm) cc_final: 0.7417 (tpt) REVERT: A 3203 MET cc_start: 0.6071 (pmm) cc_final: 0.5264 (pmm) REVERT: A 3224 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7842 (mtm-85) outliers start: 43 outliers final: 32 residues processed: 144 average time/residue: 0.4200 time to fit residues: 67.1092 Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2450 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2681 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3109 MET Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [97, 9, 74, 111, 129, 35, 101, 109, 39, 24, 21] chunk 97 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1768 GLN A1799 ASN A2302 ASN A2476 HIS A2702 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093766 restraints weight = 16184.055| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.61 r_work: 0.3082 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10826 Z= 0.130 Angle : 0.557 13.761 14639 Z= 0.277 Chirality : 0.039 0.165 1707 Planarity : 0.004 0.050 1858 Dihedral : 3.799 18.132 1453 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.94 % Allowed : 25.71 % Favored : 71.34 % 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: 1.47 (0.23), residues: 1332 helix: 2.06 (0.18), residues: 800 sheet: 0.63 (0.64), residues: 74 loop : -0.97 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1638 TYR 0.025 0.001 TYR A1054 PHE 0.022 0.001 PHE A2633 TRP 0.017 0.001 TRP A2542 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10820) covalent geometry : angle 0.55586 / 0.28 (14633) hydrogen bonds : bond 0.03445 / 2.31 ( 629) hydrogen bonds : angle 3.90849 / 2.73 ( 1821) metal coordination : bond 0.00313 / 0.20 ( 6) metal coordination : angle 2.17783 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7593 (ttt90) REVERT: A 1021 GLU cc_start: 0.8149 (tp30) cc_final: 0.7519 (tp30) REVERT: A 1364 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7971 (mtt-85) REVERT: A 1449 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 1478 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8328 (pmm-80) REVERT: A 1610 ASP cc_start: 0.8020 (m-30) cc_final: 0.7799 (m-30) REVERT: A 1647 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: A 2579 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 2996 HIS cc_start: 0.8262 (t-90) cc_final: 0.7658 (t70) REVERT: A 3109 MET cc_start: 0.6306 (mpp) cc_final: 0.5832 (mtm) REVERT: A 3139 MET cc_start: 0.7701 (ttm) cc_final: 0.7404 (tpt) REVERT: A 3203 MET cc_start: 0.6061 (pmm) cc_final: 0.5357 (pmm) REVERT: A 3224 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7827 (mtm-85) outliers start: 35 outliers final: 27 residues processed: 145 average time/residue: 0.4513 time to fit residues: 72.0392 Evaluate side-chains 144 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2450 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [111, 101, 7, 1, 27, 86, 117, 98, 9, 127, 65] chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1401 ASN A1768 GLN A1799 ASN A2702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094379 restraints weight = 15984.125| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.62 r_work: 0.3099 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10826 Z= 0.118 Angle : 0.542 12.524 14639 Z= 0.270 Chirality : 0.039 0.170 1707 Planarity : 0.003 0.050 1858 Dihedral : 3.751 16.975 1453 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.86 % Allowed : 25.97 % Favored : 71.18 % 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: 1.55 (0.23), residues: 1332 helix: 2.12 (0.18), residues: 800 sheet: 0.76 (0.64), residues: 74 loop : -0.92 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1638 TYR 0.009 0.001 TYR A1503 PHE 0.020 0.001 PHE A2633 TRP 0.018 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10820) covalent geometry : angle 0.53988 / 0.27 (14633) hydrogen bonds : bond 0.03319 / 2.22 ( 629) hydrogen bonds : angle 3.84954 / 2.69 ( 1821) metal coordination : bond 0.00277 / 0.17 ( 6) metal coordination : angle 2.36186 / 1.41 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 990 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7566 (ttt90) REVERT: A 1021 GLU cc_start: 0.8081 (tp30) cc_final: 0.7489 (tp30) REVERT: A 1449 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 2579 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8010 (mt-10) REVERT: A 2996 HIS cc_start: 0.8253 (t-90) cc_final: 0.7650 (t70) REVERT: A 3109 MET cc_start: 0.6343 (mpp) cc_final: 0.5841 (mtm) REVERT: A 3139 MET cc_start: 0.7709 (ttm) cc_final: 0.7405 (tpt) REVERT: A 3203 MET cc_start: 0.6070 (pmm) cc_final: 0.5415 (pmm) REVERT: A 3224 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7839 (mtm-85) outliers start: 34 outliers final: 26 residues processed: 146 average time/residue: 0.4272 time to fit residues: 69.0946 Evaluate side-chains 139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2450 VAL Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3012 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3107 VAL Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3177 HIS Chi-restraints excluded: chain A residue 3224 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: [90, 111, 35, 63, 71, 117, 18, 105, 101, 118, 28] chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1768 GLN A1799 ASN A2302 ASN A2702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094663 restraints weight = 16094.882| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.62 r_work: 0.3099 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10826 Z= 0.128 Angle : 0.556 15.518 14639 Z= 0.278 Chirality : 0.040 0.170 1707 Planarity : 0.003 0.050 1858 Dihedral : 3.733 17.088 1453 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.86 % Allowed : 25.88 % Favored : 71.26 % 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: 1.55 (0.23), residues: 1332 helix: 2.10 (0.18), residues: 800 sheet: 0.79 (0.64), residues: 74 loop : -0.92 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A1638 TYR 0.019 0.001 TYR A1054 PHE 0.020 0.001 PHE A2633 TRP 0.018 0.001 TRP A2542 HIS 0.004 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10820) covalent geometry : angle 0.55424 / 0.28 (14633) hydrogen bonds : bond 0.03330 / 2.22 ( 629) hydrogen bonds : angle 3.86836 / 2.70 ( 1821) metal coordination : bond 0.00293 / 0.18 ( 6) metal coordination : angle 2.42035 / 1.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.89 seconds wall clock time: 57 minutes 54.47 seconds (3474.47 seconds total)