Starting phenix.real_space_refine on Sat Oct 24 05:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.cif Found real_map, /net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.map" model { file = "/net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22th_68657/10_2026/22th_68657.cif" } resolution = 2.5 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= 0.006 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 95 5.16 5 C 7478 2.51 5 N 2025 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11814 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 11563 Classifications: {'peptide': 1530} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 45, 'TRANS': 1484} Chain breaks: 15 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 850 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 34, 'ASP:plan': 15, 'ARG:plan': 18, 'ASN:plan1': 9, 'TYR:plan': 4, 'GLN:plan1': 6, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 385 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 251 Unusual residues: {' MG': 1, ' MN': 1, ' ZN': 2, 'SVR': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 269 Planarities with less than four sites: {'SVR:plan-3': 3, 'SVR:plan-4': 3, 'SVR:plan-7': 2, 'SVR:plan-9': 3, 'SVR:plan-8': 2, 'SVR:plan-10': 2, 'SVR:plan-2': 2, 'SVR:plan-6': 2, 'SVR:plan-1': 1, 'SVR:plan-5': 1, 'SVR:plan-11': 1} Unresolved non-hydrogen planarities: 176 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 789 SG CYS A1028 65.433 25.169 90.478 1.00 85.29 S ATOM 804 SG CYS A1031 69.052 26.292 90.607 1.00 89.27 S ATOM 1039 SG CYS A1062 68.163 22.915 89.058 1.00 91.85 S ATOM 1059 SG CYS A1065 67.233 26.119 87.269 1.00 95.03 S ATOM 2212 SG CYS A1294 67.815 45.406 41.403 1.00 63.30 S Time building chain proxies: 2.73, per 1000 atoms: 0.23 Number of scatterers: 11814 At special positions: 0 Unit cell: (98.55, 102.93, 131.4, 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 95 16.00 Mg 1 11.99 O 2212 8.00 N 2025 7.00 C 7478 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: 1.01 Conformation dependent library (CDL) restraints added in 472.6 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 A1028 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " 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 " pdb="ZN ZN A4002 " - pdb=" ND1 HIS A1365 " Number of angles added : 6 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 9 sheets defined 65.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 5.176A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.421A 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: 3.989A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1041 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.565A pdb=" N GLN A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1061 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.564A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1105 through 1112 Processing helix chain 'A' and resid 1119 through 1139 Processing helix chain 'A' and resid 1174 through 1192 Processing helix chain 'A' and resid 1198 through 1209 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.532A pdb=" N LEU A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1296 Processing helix chain 'A' and resid 1297 through 1309 Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 3.819A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1435 removed outlier: 3.503A pdb=" N VAL A1431 " --> pdb=" O CYS A1428 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) removed outlier: 4.145A 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 removed outlier: 3.548A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.979A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1531 removed outlier: 4.046A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.257A 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: 3.797A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.451A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.070A 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 removed outlier: 3.821A pdb=" N THR A1635 " --> pdb=" O VAL A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 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 1806 Processing helix chain 'A' and resid 1807 through 1810 Processing helix chain 'A' and resid 1835 through 1846 Processing helix chain 'A' and resid 2295 through 2306 removed outlier: 3.727A pdb=" N THR A2306 " --> pdb=" O ASN A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2370 through 2379 Processing helix chain 'A' and resid 2382 through 2397 Processing helix chain 'A' and resid 2404 through 2418 removed outlier: 3.504A pdb=" N ILE A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A2414 " --> pdb=" O LYS A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2440 Processing helix chain 'A' and resid 2441 through 2445 Processing helix chain 'A' and resid 2448 through 2457 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.772A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2559 removed outlier: 4.858A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.603A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.674A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.605A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.262A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 Processing helix chain 'A' and resid 2671 through 2675 removed outlier: 3.850A pdb=" N VAL A2675 " --> pdb=" O SER A2672 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 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 removed outlier: 3.562A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2900 through 2911 Processing helix chain 'A' and resid 2951 through 2955 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 3073 Processing helix chain 'A' and resid 3093 through 3099 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3115 through 3122 removed outlier: 4.010A 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 3142 removed outlier: 3.597A pdb=" N PHE A3142 " --> pdb=" O ILE A3138 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3185 Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.576A pdb=" N LEU A3212 " --> pdb=" O THR A3208 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 970 through 972 removed outlier: 3.506A pdb=" N TYR A1755 " --> pdb=" O VAL A 971 " (cutoff:3.500A) 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 1219 through 1220 removed outlier: 3.634A pdb=" N VAL A1220 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A1358 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2507 through 2515 removed outlier: 4.109A pdb=" N TYR A2519 " --> pdb=" O GLY A2357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2399 through 2402 removed outlier: 3.673A pdb=" N ARG A2399 " --> pdb=" O SER A2467 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.560A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3004 through 3009 removed outlier: 5.939A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3078 through 3081 removed outlier: 3.722A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3086 through 3089 720 hydrogen bonds defined for protein. 2082 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: 2.19 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3200 1.33 - 1.45: 2072 1.45 - 1.57: 6619 1.57 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 12020 Sorted by residual: bond pdb=" N GLU A3038 " pdb=" CA GLU A3038 " ideal model delta sigma weight residual 1.455 1.477 -0.021 1.25e-02 6.40e+03 2.89e+00 bond pdb=" C GLU A3038 " pdb=" O GLU A3038 " ideal model delta sigma weight residual 1.235 1.247 -0.013 1.22e-02 6.72e+03 1.07e+00 bond pdb=" CB ASN A2447 " pdb=" CG ASN A2447 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 bond pdb=" CA PHE A2633 " pdb=" CB PHE A2633 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.66e-02 3.63e+03 9.28e-01 bond pdb=" CG1 ILE A1363 " pdb=" CD1 ILE A1363 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.85e-01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 16189 1.78 - 3.55: 131 3.55 - 5.33: 12 5.33 - 7.10: 6 7.10 - 8.88: 1 Bond angle restraints: 16339 Sorted by residual: angle pdb=" C ASN A2348 " pdb=" CA ASN A2348 " pdb=" CB ASN A2348 " ideal model delta sigma weight residual 109.53 114.77 -5.24 1.65e+00 3.67e-01 1.01e+01 angle pdb=" C PRO A2364 " pdb=" N ILE A2365 " pdb=" CA ILE A2365 " ideal model delta sigma weight residual 121.97 127.31 -5.34 1.80e+00 3.09e-01 8.80e+00 angle pdb=" CA ASN A2447 " pdb=" CB ASN A2447 " pdb=" CG ASN A2447 " ideal model delta sigma weight residual 112.60 115.17 -2.57 1.00e+00 1.00e+00 6.60e+00 angle pdb=" CA LEU A3092 " pdb=" CB LEU A3092 " pdb=" CG LEU A3092 " ideal model delta sigma weight residual 116.30 125.18 -8.88 3.50e+00 8.16e-02 6.44e+00 angle pdb=" CA ASN A2348 " pdb=" CB ASN A2348 " pdb=" CG ASN A2348 " ideal model delta sigma weight residual 112.60 114.92 -2.32 1.00e+00 1.00e+00 5.37e+00 ... (remaining 16334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6207 17.94 - 35.87: 691 35.87 - 53.81: 192 53.81 - 71.74: 38 71.74 - 89.68: 17 Dihedral angle restraints: 7145 sinusoidal: 2654 harmonic: 4491 Sorted by residual: dihedral pdb=" CA SER A2516 " pdb=" C SER A2516 " pdb=" N ASP A2517 " pdb=" CA ASP A2517 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLU A2579 " pdb=" C GLU A2579 " pdb=" N PHE A2580 " pdb=" CA PHE A2580 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB GLU A2297 " pdb=" CG GLU A2297 " pdb=" CD GLU A2297 " pdb=" OE1 GLU A2297 " ideal model delta sinusoidal sigma weight residual 0.00 -88.71 88.71 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1251 0.027 - 0.055: 393 0.055 - 0.082: 162 0.082 - 0.109: 64 0.109 - 0.136: 22 Chirality restraints: 1892 Sorted by residual: chirality pdb=" CA ILE A1363 " pdb=" N ILE A1363 " pdb=" C ILE A1363 " pdb=" CB ILE A1363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-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 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE A2528 " pdb=" N ILE A2528 " pdb=" C ILE A2528 " pdb=" CB ILE A2528 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1889 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A2348 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ASN A2348 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A2348 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A2349 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A3021 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO A3022 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A3022 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A3022 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A2447 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ASN A2447 " -0.020 2.00e-02 2.50e+03 pdb=" O ASN A2447 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP A2448 " 0.007 2.00e-02 2.50e+03 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 123 2.59 - 3.17: 9868 3.17 - 3.75: 19750 3.75 - 4.32: 26630 4.32 - 4.90: 43753 Nonbonded interactions: 100124 Sorted by model distance: nonbonded pdb=" OE2 GLU A3081 " pdb="MG MG A4004 " model vdw 2.018 2.170 nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.019 2.230 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.110 2.320 nonbonded pdb=" OE1 GLU A2575 " pdb="MN MN A4003 " model vdw 2.125 2.320 nonbonded pdb=" O ARG A1427 " pdb="MG MG A4004 " model vdw 2.141 2.170 ... (remaining 100119 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: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.080 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 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 0.035 12027 Z= 0.088 Angle : 0.423 8.879 16345 Z= 0.221 Chirality : 0.036 0.136 1892 Planarity : 0.003 0.040 2063 Dihedral : 17.166 89.678 4209 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 0.41 % Allowed : 22.82 % Favored : 76.77 % 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: 2.62 (0.22), residues: 1498 helix: 2.83 (0.17), residues: 897 sheet: 1.62 (0.59), residues: 81 loop : -0.25 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1456 TYR 0.008 0.001 TYR A3196 PHE 0.015 0.001 PHE A2633 TRP 0.010 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (12020) covalent geometry : angle 0.42284 / 0.22 (16339) hydrogen bonds : bond 0.10027 / 6.80 ( 720) hydrogen bonds : angle 4.34375 / 3.19 ( 2082) metal coordination : bond 0.00241 / 0.14 ( 7) metal coordination : angle 0.50483 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.467 Fit side-chains REVERT: A 1802 LYS cc_start: 0.8764 (tttm) cc_final: 0.8558 (ttmm) REVERT: A 2607 GLN cc_start: 0.7533 (tt0) cc_final: 0.7317 (tm-30) REVERT: A 3023 ASN cc_start: 0.8780 (t0) cc_final: 0.8554 (t0) REVERT: A 3140 GLN cc_start: 0.7504 (mp10) cc_final: 0.7240 (mp10) outliers start: 5 outliers final: 3 residues processed: 130 average time/residue: 0.4311 time to fit residues: 62.8921 Evaluate side-chains 122 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2596 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 GLN ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN A2822 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085174 restraints weight = 17563.595| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.36 r_work: 0.2890 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12027 Z= 0.131 Angle : 0.461 6.919 16345 Z= 0.240 Chirality : 0.039 0.149 1892 Planarity : 0.003 0.033 2063 Dihedral : 5.918 75.561 1653 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 21.51 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.46 (0.22), residues: 1498 helix: 2.72 (0.17), residues: 910 sheet: 1.52 (0.58), residues: 81 loop : -0.43 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1222 TYR 0.010 0.001 TYR A1503 PHE 0.021 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12020) covalent geometry : angle 0.46064 / 0.24 (16339) hydrogen bonds : bond 0.03264 / 2.23 ( 720) hydrogen bonds : angle 3.73106 / 2.75 ( 2082) metal coordination : bond 0.00748 / 0.42 ( 7) metal coordination : angle 1.38011 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.461 Fit side-chains REVERT: A 1382 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7637 (mtm) REVERT: A 1644 LEU cc_start: 0.8895 (mt) cc_final: 0.8591 (mt) REVERT: A 1802 LYS cc_start: 0.8449 (tttm) cc_final: 0.8206 (ttmm) REVERT: A 2646 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 3140 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7235 (mp10) outliers start: 27 outliers final: 5 residues processed: 144 average time/residue: 0.4782 time to fit residues: 76.3264 Evaluate side-chains 129 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3140 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [98, 146, 27, 57, 104, 126, 76, 77, 135, 31, 18] chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1425 GLN A2348 ASN ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2822 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084307 restraints weight = 17507.868| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.34 r_work: 0.2868 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12027 Z= 0.121 Angle : 0.445 6.865 16345 Z= 0.231 Chirality : 0.038 0.155 1892 Planarity : 0.003 0.038 2063 Dihedral : 5.858 73.987 1648 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 2.13 % Allowed : 22.66 % Favored : 75.21 % 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: 2.41 (0.22), residues: 1498 helix: 2.66 (0.17), residues: 916 sheet: 1.45 (0.58), residues: 81 loop : -0.45 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1222 TYR 0.009 0.001 TYR A2652 PHE 0.023 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12020) covalent geometry : angle 0.44463 / 0.23 (16339) hydrogen bonds : bond 0.03224 / 2.21 ( 720) hydrogen bonds : angle 3.66209 / 2.70 ( 2082) metal coordination : bond 0.00681 / 0.39 ( 7) metal coordination : angle 1.26518 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.573 Fit side-chains REVERT: A 1382 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7599 (mtm) REVERT: A 1605 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7511 (mtp85) REVERT: A 1802 LYS cc_start: 0.8459 (tttm) cc_final: 0.8205 (ttmm) REVERT: A 2646 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: A 2744 PHE cc_start: 0.7739 (t80) cc_final: 0.7504 (t80) REVERT: A 2953 MET cc_start: 0.6770 (tpt) cc_final: 0.6542 (tpt) REVERT: A 3140 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7255 (mp10) outliers start: 26 outliers final: 7 residues processed: 141 average time/residue: 0.4595 time to fit residues: 72.0309 Evaluate side-chains 127 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [77, 139, 59, 147, 72, 144, 17, 98, 39, 78, 5] chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 ASN A2396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084614 restraints weight = 17453.098| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.33 r_work: 0.2874 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12027 Z= 0.108 Angle : 0.437 6.750 16345 Z= 0.226 Chirality : 0.038 0.164 1892 Planarity : 0.003 0.037 2063 Dihedral : 5.841 73.108 1648 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 22.74 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.22), residues: 1498 helix: 2.67 (0.17), residues: 916 sheet: 1.45 (0.57), residues: 81 loop : -0.44 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1222 TYR 0.009 0.001 TYR A1413 PHE 0.023 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.003 0.000 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12020) covalent geometry : angle 0.43630 / 0.23 (16339) hydrogen bonds : bond 0.03051 / 2.09 ( 720) hydrogen bonds : angle 3.60293 / 2.66 ( 2082) metal coordination : bond 0.00580 / 0.31 ( 7) metal coordination : angle 1.57244 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.483 Fit side-chains REVERT: A 1392 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7620 (mp0) REVERT: A 1802 LYS cc_start: 0.8462 (tttm) cc_final: 0.8207 (ttmm) REVERT: A 2646 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 2744 PHE cc_start: 0.7717 (t80) cc_final: 0.7436 (t80) REVERT: A 3140 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7328 (mp10) outliers start: 24 outliers final: 8 residues processed: 139 average time/residue: 0.4376 time to fit residues: 67.6490 Evaluate side-chains 130 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [92, 28, 93, 113, 101, 53, 129, 104, 41, 103, 37] chunk 92 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 ASN A2822 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083477 restraints weight = 17423.778| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.32 r_work: 0.2852 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12027 Z= 0.123 Angle : 0.448 6.815 16345 Z= 0.232 Chirality : 0.038 0.166 1892 Planarity : 0.003 0.040 2063 Dihedral : 5.855 72.530 1648 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.63 % Allowed : 22.66 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.38 (0.22), residues: 1498 helix: 2.64 (0.17), residues: 916 sheet: 1.44 (0.57), residues: 81 loop : -0.47 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1222 TYR 0.009 0.001 TYR A1413 PHE 0.025 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.003 0.000 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (12020) covalent geometry : angle 0.44730 / 0.23 (16339) hydrogen bonds : bond 0.03203 / 2.20 ( 720) hydrogen bonds : angle 3.63175 / 2.69 ( 2082) metal coordination : bond 0.00603 / 0.35 ( 7) metal coordination : angle 1.47241 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 1392 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7602 (mp0) REVERT: A 1605 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7523 (mtp85) REVERT: A 1640 MET cc_start: 0.9220 (tmm) cc_final: 0.9014 (ttp) REVERT: A 1802 LYS cc_start: 0.8455 (tttm) cc_final: 0.8203 (ttmm) REVERT: A 2448 ASP cc_start: 0.8687 (m-30) cc_final: 0.8384 (m-30) REVERT: A 2646 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: A 2744 PHE cc_start: 0.7708 (t80) cc_final: 0.7440 (t80) REVERT: A 2953 MET cc_start: 0.6789 (tpt) cc_final: 0.6537 (tpp) REVERT: A 3140 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7364 (mp10) outliers start: 32 outliers final: 10 residues processed: 146 average time/residue: 0.4610 time to fit residues: 74.6256 Evaluate side-chains 132 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [98, 108, 84, 63, 89, 101, 22, 20, 25, 121, 59] chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.0040 chunk 121 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN A1401 ASN A2348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083938 restraints weight = 17482.518| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.33 r_work: 0.2861 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12027 Z= 0.109 Angle : 0.446 6.721 16345 Z= 0.230 Chirality : 0.038 0.168 1892 Planarity : 0.003 0.047 2063 Dihedral : 5.853 72.568 1648 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 2.30 % Allowed : 23.15 % Favored : 74.55 % 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: 2.40 (0.22), residues: 1498 helix: 2.66 (0.17), residues: 916 sheet: 1.45 (0.57), residues: 81 loop : -0.48 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.024 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12020) covalent geometry : angle 0.44497 / 0.23 (16339) hydrogen bonds : bond 0.03074 / 2.11 ( 720) hydrogen bonds : angle 3.59938 / 2.67 ( 2082) metal coordination : bond 0.00476 / 0.27 ( 7) metal coordination : angle 1.41249 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.497 Fit side-chains REVERT: A 1135 MET cc_start: 0.8878 (ttp) cc_final: 0.8468 (ptm) REVERT: A 1392 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7626 (mp0) REVERT: A 1605 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7519 (mtp85) REVERT: A 1802 LYS cc_start: 0.8460 (tttm) cc_final: 0.8207 (ttmm) REVERT: A 2646 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: A 2744 PHE cc_start: 0.7709 (t80) cc_final: 0.7406 (t80) REVERT: A 3140 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7325 (mp10) outliers start: 28 outliers final: 13 residues processed: 144 average time/residue: 0.4618 time to fit residues: 74.1750 Evaluate side-chains 132 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [24, 116, 101, 112, 130, 103, 77, 5, 146, 15, 43] chunk 24 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 146 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN A2348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082709 restraints weight = 17336.421| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.32 r_work: 0.2844 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12027 Z= 0.133 Angle : 0.468 6.836 16345 Z= 0.242 Chirality : 0.039 0.173 1892 Planarity : 0.003 0.047 2063 Dihedral : 5.878 72.969 1648 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 2.46 % Allowed : 22.91 % Favored : 74.63 % 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: 2.37 (0.22), residues: 1498 helix: 2.64 (0.17), residues: 916 sheet: 1.38 (0.56), residues: 85 loop : -0.47 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.026 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12020) covalent geometry : angle 0.46723 / 0.24 (16339) hydrogen bonds : bond 0.03299 / 2.28 ( 720) hydrogen bonds : angle 3.67190 / 2.73 ( 2082) metal coordination : bond 0.00639 / 0.36 ( 7) metal coordination : angle 1.45879 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.523 Fit side-chains REVERT: A 1135 MET cc_start: 0.8893 (ttp) cc_final: 0.8490 (ptm) REVERT: A 1222 ARG cc_start: 0.8351 (ptm160) cc_final: 0.7859 (ttp-110) REVERT: A 1392 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7621 (mp0) REVERT: A 1605 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7548 (mtp85) REVERT: A 1640 MET cc_start: 0.9213 (tmm) cc_final: 0.8956 (ttp) REVERT: A 1802 LYS cc_start: 0.8454 (tttm) cc_final: 0.8205 (ttmm) REVERT: A 2440 ASN cc_start: 0.8860 (m-40) cc_final: 0.8576 (p0) REVERT: A 2744 PHE cc_start: 0.7700 (t80) cc_final: 0.7383 (t80) REVERT: A 3140 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7296 (mp10) outliers start: 30 outliers final: 15 residues processed: 143 average time/residue: 0.4531 time to fit residues: 72.1658 Evaluate side-chains 134 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2348 ASN Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [41, 130, 152, 86, 140, 59, 10, 79, 12, 20, 56] chunk 41 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN A2348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081397 restraints weight = 17481.128| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.33 r_work: 0.2815 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12027 Z= 0.160 Angle : 0.488 7.059 16345 Z= 0.252 Chirality : 0.040 0.183 1892 Planarity : 0.003 0.046 2063 Dihedral : 5.923 73.212 1648 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 2.30 % Allowed : 23.07 % Favored : 74.63 % 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: 2.27 (0.22), residues: 1498 helix: 2.57 (0.17), residues: 916 sheet: 1.17 (0.58), residues: 83 loop : -0.51 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.029 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.003 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (12020) covalent geometry : angle 0.48748 / 0.25 (16339) hydrogen bonds : bond 0.03513 / 2.44 ( 720) hydrogen bonds : angle 3.75337 / 2.79 ( 2082) metal coordination : bond 0.00795 / 0.44 ( 7) metal coordination : angle 1.49105 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 1392 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7661 (mp0) REVERT: A 1605 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: A 1640 MET cc_start: 0.9209 (tmm) cc_final: 0.9003 (ttp) REVERT: A 1802 LYS cc_start: 0.8451 (tttm) cc_final: 0.8209 (ttmm) REVERT: A 2744 PHE cc_start: 0.7686 (t80) cc_final: 0.7337 (t80) REVERT: A 3140 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7307 (mp10) outliers start: 28 outliers final: 14 residues processed: 138 average time/residue: 0.4199 time to fit residues: 64.8141 Evaluate side-chains 131 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2348 ASN Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [111, 114, 110, 54, 15, 131, 34, 49, 85, 101, 148] chunk 111 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN A2348 ASN ** A2607 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.121890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083259 restraints weight = 17242.092| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.32 r_work: 0.2852 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12027 Z= 0.108 Angle : 0.464 6.856 16345 Z= 0.239 Chirality : 0.038 0.183 1892 Planarity : 0.003 0.056 2063 Dihedral : 5.887 73.059 1648 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 1.72 % Allowed : 23.73 % Favored : 74.55 % 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: 2.32 (0.22), residues: 1498 helix: 2.60 (0.17), residues: 916 sheet: 1.20 (0.58), residues: 83 loop : -0.48 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.025 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12020) covalent geometry : angle 0.46321 / 0.24 (16339) hydrogen bonds : bond 0.03147 / 2.17 ( 720) hydrogen bonds : angle 3.68376 / 2.74 ( 2082) metal coordination : bond 0.00464 / 0.26 ( 7) metal coordination : angle 1.48111 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 1135 MET cc_start: 0.8904 (ttp) cc_final: 0.8503 (ptm) REVERT: A 1222 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7878 (ttp-110) REVERT: A 1392 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7661 (mp0) REVERT: A 1605 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7460 (mtp85) REVERT: A 1802 LYS cc_start: 0.8435 (tttm) cc_final: 0.8193 (ttmm) REVERT: A 2448 ASP cc_start: 0.8649 (m-30) cc_final: 0.8350 (m-30) REVERT: A 2744 PHE cc_start: 0.7673 (t80) cc_final: 0.7324 (t80) REVERT: A 3140 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7199 (mp10) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.4389 time to fit residues: 64.8977 Evaluate side-chains 129 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1150 GLN Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [125, 9, 10, 36, 93, 51, 114, 106, 44, 71, 62] chunk 125 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN A2348 ASN ** A2607 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.121788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083386 restraints weight = 17427.957| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.33 r_work: 0.2850 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12027 Z= 0.112 Angle : 0.467 6.808 16345 Z= 0.240 Chirality : 0.038 0.187 1892 Planarity : 0.003 0.057 2063 Dihedral : 5.879 73.243 1648 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.56 % Allowed : 24.06 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.22), residues: 1498 helix: 2.60 (0.17), residues: 917 sheet: 1.20 (0.58), residues: 79 loop : -0.54 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.025 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12020) covalent geometry : angle 0.46675 / 0.24 (16339) hydrogen bonds : bond 0.03148 / 2.16 ( 720) hydrogen bonds : angle 3.66687 / 2.73 ( 2082) metal coordination : bond 0.00512 / 0.28 ( 7) metal coordination : angle 1.44664 / 0.86 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 1135 MET cc_start: 0.8899 (ttp) cc_final: 0.8502 (ptm) REVERT: A 1222 ARG cc_start: 0.8347 (ptm160) cc_final: 0.7886 (ttp-110) REVERT: A 1392 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7663 (mp0) REVERT: A 1605 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7523 (mtp85) REVERT: A 1802 LYS cc_start: 0.8437 (tttm) cc_final: 0.8195 (ttmm) REVERT: A 2744 PHE cc_start: 0.7677 (t80) cc_final: 0.7329 (t80) REVERT: A 3140 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7205 (mp10) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.4325 time to fit residues: 62.8304 Evaluate side-chains 128 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 2348 ASN Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2755 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3140 GLN Chi-restraints excluded: chain A residue 3209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [39, 90, 148, 83, 106, 12, 143, 1, 48, 85, 56] chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 143 optimal weight: 0.0170 chunk 1 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2607 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.121799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083361 restraints weight = 17532.921| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.35 r_work: 0.2854 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 12027 Z= 0.169 Angle : 0.767 59.196 16345 Z= 0.452 Chirality : 0.042 0.800 1892 Planarity : 0.003 0.054 2063 Dihedral : 5.916 73.243 1648 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.48 % Allowed : 24.14 % Favored : 74.38 % Cbeta Deviations : 0.07 % 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: 2.31 (0.22), residues: 1498 helix: 2.60 (0.17), residues: 917 sheet: 1.25 (0.58), residues: 79 loop : -0.50 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1222 TYR 0.010 0.001 TYR A1413 PHE 0.025 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.002 0.000 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12020) covalent geometry : angle 0.76678 / 0.45 (16339) hydrogen bonds : bond 0.03149 / 2.16 ( 720) hydrogen bonds : angle 3.66482 / 2.72 ( 2082) metal coordination : bond 0.00504 / 0.28 ( 7) metal coordination : angle 1.44436 / 0.86 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.81 seconds wall clock time: 84 minutes 4.40 seconds (5044.40 seconds total)