Starting phenix.real_space_refine on Sat Oct 24 04:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.cif Found real_map, /net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.map" model { file = "/net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26ka_80707/10_2026/26ka_80707.cif" } resolution = 3.03 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= 0.015 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: 8 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 85 5.16 5 C 7408 2.51 5 N 2004 2.21 5 O 2241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 11752 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1497, 11537 Classifications: {'peptide': 1497} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 44, 'TRANS': 1452} Chain breaks: 16 Unresolved non-hydrogen bonds: 446 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 20, 'GLU:plan': 22, 'ASN:plan1': 2, 'TYR:plan': 3, 'GLN:plan1': 8, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 274 Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 6} 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 803 SG CYS A1028 44.740 17.707 90.924 1.00102.93 S ATOM 822 SG CYS A1031 47.664 15.412 91.174 1.00103.24 S ATOM 1065 SG CYS A1062 44.470 14.016 89.773 1.00108.27 S ATOM 1085 SG CYS A1065 46.398 16.538 87.713 1.00103.48 S ATOM 2318 SG CYS A1294 57.714 26.613 40.051 1.00 95.04 S Time building chain proxies: 2.38, per 1000 atoms: 0.20 Number of scatterers: 11752 At special positions: 0 Unit cell: (115.34, 102.2, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 85 16.00 P 10 15.00 Mg 1 11.99 O 2241 8.00 N 2004 7.00 C 7408 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: 0.96 Conformation dependent library (CDL) restraints added in 511.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " 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 ZN A4001 " - pdb=" SG CYS A1065 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " Number of angles added : 6 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 10 sheets defined 64.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.624A pdb=" N VAL A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.565A 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 1024 Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.636A 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: 3.875A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 3.919A pdb=" N ARG A1111 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1140 Processing helix chain 'A' and resid 1176 through 1194 Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1266 through 1277 Processing helix chain 'A' and resid 1278 through 1282 removed outlier: 3.682A pdb=" N LYS A1282 " --> pdb=" O PHE A1279 " (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 1329 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 4.288A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1435 removed outlier: 3.999A 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: 3.539A 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: 3.916A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1531 removed outlier: 4.042A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.255A 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: 3.810A 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: 3.937A 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 1629 through 1651 removed outlier: 3.640A pdb=" N GLU A1634 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A1635 " --> pdb=" O VAL A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 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 1796 through 1805 Processing helix chain 'A' and resid 2295 through 2305 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 2404 through 2417 removed outlier: 3.766A pdb=" N ILE A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2436 through 2440 Processing helix chain 'A' and resid 2441 through 2444 Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.749A pdb=" N LYS A2451 " --> pdb=" O ASN A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.962A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2559 removed outlier: 4.954A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.583A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.669A 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: 3.714A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.754A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2659 No H-bonds generated for 'chain 'A' and resid 2658 through 2659' Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.634A 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 2753 through 2765 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 2912 Processing helix chain 'A' and resid 2994 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 3114 through 3122 removed outlier: 3.694A pdb=" N ILE A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) removed outlier: 3.554A 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 Processing helix chain 'A' and resid 3142 through 3158 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: 3.678A 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: 6.603A 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 1143 through 1145 Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.033A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET A1382 " --> pdb=" O PHE A1398 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE A1398 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS A1384 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY A1396 " --> pdb=" O CYS A1384 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A1386 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2514 Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2402 Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.549A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.692A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3078 through 3081 removed outlier: 4.092A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089 699 hydrogen bonds defined for protein. 2022 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: 2.41 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3787 1.34 - 1.46: 1596 1.46 - 1.58: 6441 1.58 - 1.69: 19 1.69 - 1.81: 121 Bond restraints: 11964 Sorted by residual: bond pdb=" P U B 10 " pdb=" O5' U B 10 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.08e+00 bond pdb=" N VAL A1670 " pdb=" CA VAL A1670 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.41e-02 5.03e+03 6.91e+00 bond pdb=" N ASN A2857 " pdb=" CA ASN A2857 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.59e+00 bond pdb=" N LYS A2858 " pdb=" CA LYS A2858 " ideal model delta sigma weight residual 1.455 1.483 -0.029 1.29e-02 6.01e+03 4.93e+00 bond pdb=" N THR A2659 " pdb=" CA THR A2659 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.09e-02 8.42e+03 4.81e+00 ... (remaining 11959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16040 2.01 - 4.03: 173 4.03 - 6.04: 28 6.04 - 8.05: 4 8.05 - 10.07: 1 Bond angle restraints: 16246 Sorted by residual: angle pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " ideal model delta sigma weight residual 108.20 112.82 -4.62 8.00e-01 1.56e+00 3.33e+01 angle pdb=" C SER A2602 " pdb=" N VAL A2603 " pdb=" CA VAL A2603 " ideal model delta sigma weight residual 121.97 129.85 -7.88 1.80e+00 3.09e-01 1.92e+01 angle pdb=" C1' C B 4 " pdb=" N1 C B 4 " pdb=" C2 C B 4 " ideal model delta sigma weight residual 118.80 123.50 -4.70 1.10e+00 8.26e-01 1.83e+01 angle pdb=" C LYS A2858 " pdb=" N ILE A2859 " pdb=" CA ILE A2859 " ideal model delta sigma weight residual 122.72 117.45 5.27 1.39e+00 5.18e-01 1.43e+01 angle pdb=" N1 U B 10 " pdb=" C2 U B 10 " pdb=" O2 U B 10 " ideal model delta sigma weight residual 122.80 125.40 -2.60 7.00e-01 2.04e+00 1.38e+01 ... (remaining 16241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 6913 31.32 - 62.65: 319 62.65 - 93.97: 19 93.97 - 125.29: 0 125.29 - 156.61: 2 Dihedral angle restraints: 7253 sinusoidal: 2859 harmonic: 4394 Sorted by residual: dihedral pdb=" O4' C B 4 " pdb=" C1' C B 4 " pdb=" N1 C B 4 " pdb=" C2 C B 4 " ideal model delta sinusoidal sigma weight residual 200.00 43.39 156.61 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual -128.00 3.98 -131.98 1 1.70e+01 3.46e-03 5.54e+01 dihedral pdb=" CA ASP A2518 " pdb=" CB ASP A2518 " pdb=" CG ASP A2518 " pdb=" OD1 ASP A2518 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1902 0.109 - 0.218: 29 0.218 - 0.328: 0 0.328 - 0.437: 0 0.437 - 0.546: 2 Chirality restraints: 1933 Sorted by residual: chirality pdb=" P U B 10 " pdb=" OP1 U B 10 " pdb=" OP2 U B 10 " pdb=" O5' U B 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CB VAL A2603 " pdb=" CA VAL A2603 " pdb=" CG1 VAL A2603 " pdb=" CG2 VAL A2603 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA CYS A1091 " pdb=" N CYS A1091 " pdb=" C CYS A1091 " pdb=" CB CYS A1091 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 1930 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A2602 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C SER A2602 " 0.043 2.00e-02 2.50e+03 pdb=" O SER A2602 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A2603 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1286 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A1287 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1287 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A1590 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C THR A1590 " 0.033 2.00e-02 2.50e+03 pdb=" O THR A1590 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A1591 " -0.011 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 139 2.64 - 3.20: 10811 3.20 - 3.77: 19523 3.77 - 4.33: 26060 4.33 - 4.90: 43147 Nonbonded interactions: 99680 Sorted by model distance: nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.071 2.230 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.129 2.320 nonbonded pdb=" OD2 ASP A2518 " pdb="MN MN A4003 " model vdw 2.146 2.320 nonbonded pdb=" OE2 GLU A2575 " pdb="MN MN A4003 " model vdw 2.159 2.320 nonbonded pdb=" OE1 GLU A2575 " pdb="MN MN A4003 " model vdw 2.160 2.320 ... (remaining 99675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.650 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.060 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11970 Z= 0.136 Angle : 0.514 10.066 16252 Z= 0.296 Chirality : 0.042 0.546 1933 Planarity : 0.003 0.055 2021 Dihedral : 16.995 156.614 4381 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 0.24 % Allowed : 21.80 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1463 helix: 2.27 (0.18), residues: 877 sheet: 0.87 (0.62), residues: 72 loop : -0.82 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2750 TYR 0.011 0.001 TYR A1054 PHE 0.017 0.001 PHE A2633 TRP 0.015 0.001 TRP A2444 HIS 0.002 0.000 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (11964) covalent geometry : angle 0.51246 / 0.30 (16246) hydrogen bonds : bond 0.11868 / 8.60 ( 699) hydrogen bonds : angle 4.61927 / 3.40 ( 2022) metal coordination : bond 0.00342 / 0.24 ( 6) metal coordination : angle 2.19672 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.475 Fit side-chains REVERT: A 1669 ASN cc_start: 0.8594 (t0) cc_final: 0.8364 (t0) outliers start: 3 outliers final: 1 residues processed: 127 average time/residue: 0.1114 time to fit residues: 20.6737 Evaluate side-chains 116 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1401 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 50.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 ASN A1034 ASN A1401 ASN A1404 GLN ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2618 GLN A2857 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094207 restraints weight = 17177.695| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.47 r_work: 0.2938 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11970 Z= 0.234 Angle : 0.550 7.261 16252 Z= 0.286 Chirality : 0.042 0.346 1933 Planarity : 0.004 0.064 2021 Dihedral : 8.800 156.559 1730 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.94 % Favored : 96.92 % Rotamer: Outliers : 2.98 % Allowed : 19.69 % Favored : 77.33 % 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: 1.50 (0.22), residues: 1463 helix: 2.07 (0.18), residues: 890 sheet: 0.70 (0.61), residues: 72 loop : -0.97 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1605 TYR 0.016 0.002 TYR A1054 PHE 0.028 0.002 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.003 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (11964) covalent geometry : angle 0.54623 / 0.29 (16246) hydrogen bonds : bond 0.04125 / 2.78 ( 699) hydrogen bonds : angle 4.09297 / 3.03 ( 2022) metal coordination : bond 0.00984 / 0.70 ( 6) metal coordination : angle 3.19315 / 2.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.459 Fit side-chains REVERT: A 1232 LEU cc_start: 0.7756 (mt) cc_final: 0.7524 (mt) REVERT: A 2462 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6192 (mp) REVERT: A 3112 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6525 (mp) outliers start: 38 outliers final: 18 residues processed: 147 average time/residue: 0.1043 time to fit residues: 22.7790 Evaluate side-chains 130 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2516 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [14, 36, 101, 116, 100, 25, 98, 76, 15, 69, 58] chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1034 ASN A2560 GLN A2611 GLN A3140 GLN A3201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096268 restraints weight = 17249.999| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.48 r_work: 0.2973 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11970 Z= 0.127 Angle : 0.467 5.899 16252 Z= 0.247 Chirality : 0.038 0.269 1933 Planarity : 0.003 0.059 2021 Dihedral : 8.695 155.330 1728 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 2.43 % Allowed : 20.71 % Favored : 76.86 % 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: 1.59 (0.22), residues: 1463 helix: 2.17 (0.18), residues: 893 sheet: 0.77 (0.61), residues: 72 loop : -1.02 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2750 TYR 0.016 0.001 TYR A1054 PHE 0.020 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11964) covalent geometry : angle 0.46497 / 0.25 (16246) hydrogen bonds : bond 0.03625 / 2.46 ( 699) hydrogen bonds : angle 3.89538 / 2.88 ( 2022) metal coordination : bond 0.00498 / 0.35 ( 6) metal coordination : angle 2.18439 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.417 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6508 (tp) REVERT: A 1583 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7855 (mtt-85) REVERT: A 2462 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6217 (mp) REVERT: A 3109 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6687 (mtm) outliers start: 31 outliers final: 15 residues processed: 149 average time/residue: 0.1063 time to fit residues: 23.3286 Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2516 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3109 MET Chi-restraints excluded: chain A residue 3139 MET Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [24, 125, 87, 123, 122, 101, 133, 32, 58, 117, 96] chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2611 GLN A3059 GLN A3140 GLN A3201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094682 restraints weight = 17274.506| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.50 r_work: 0.2966 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11970 Z= 0.159 Angle : 0.485 6.669 16252 Z= 0.253 Chirality : 0.039 0.395 1933 Planarity : 0.003 0.061 2021 Dihedral : 8.669 154.431 1728 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.75 % Allowed : 20.31 % Favored : 76.94 % 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 (0.22), residues: 1463 helix: 2.17 (0.18), residues: 892 sheet: 0.83 (0.62), residues: 72 loop : -1.06 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2814 TYR 0.015 0.001 TYR A1054 PHE 0.024 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11964) covalent geometry : angle 0.48301 / 0.25 (16246) hydrogen bonds : bond 0.03621 / 2.44 ( 699) hydrogen bonds : angle 3.87415 / 2.86 ( 2022) metal coordination : bond 0.00643 / 0.46 ( 6) metal coordination : angle 2.14818 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.469 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6541 (tp) REVERT: A 2462 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6233 (mp) REVERT: A 3011 HIS cc_start: 0.8095 (m-70) cc_final: 0.7802 (m-70) outliers start: 35 outliers final: 24 residues processed: 148 average time/residue: 0.0951 time to fit residues: 21.0943 Evaluate side-chains 143 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2516 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [144, 93, 69, 91, 7, 105, 89, 81, 1, 140, 6] chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3140 GLN A3201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094198 restraints weight = 17421.377| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.47 r_work: 0.2954 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11970 Z= 0.173 Angle : 0.492 6.148 16252 Z= 0.257 Chirality : 0.040 0.318 1933 Planarity : 0.003 0.061 2021 Dihedral : 8.643 154.155 1728 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 2.59 % Allowed : 20.86 % Favored : 76.55 % 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: 1.54 (0.22), residues: 1463 helix: 2.15 (0.17), residues: 893 sheet: 0.78 (0.61), residues: 72 loop : -1.09 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.015 0.001 TYR A1054 PHE 0.025 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (11964) covalent geometry : angle 0.49100 / 0.26 (16246) hydrogen bonds : bond 0.03676 / 2.47 ( 699) hydrogen bonds : angle 3.88696 / 2.87 ( 2022) metal coordination : bond 0.00710 / 0.50 ( 6) metal coordination : angle 2.05121 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.476 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6521 (tp) REVERT: A 2462 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6221 (mp) REVERT: A 3011 HIS cc_start: 0.8112 (m-70) cc_final: 0.7825 (m-70) outliers start: 33 outliers final: 22 residues processed: 149 average time/residue: 0.0949 time to fit residues: 21.3600 Evaluate side-chains 138 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2516 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [44, 2, 30, 12, 89, 72, 67, 22, 15, 11, 19] chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094418 restraints weight = 17302.404| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.50 r_work: 0.2953 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11970 Z= 0.147 Angle : 0.482 9.632 16252 Z= 0.250 Chirality : 0.039 0.261 1933 Planarity : 0.003 0.061 2021 Dihedral : 8.584 153.648 1728 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.51 % Allowed : 21.41 % Favored : 76.08 % 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: 1.57 (0.22), residues: 1463 helix: 2.17 (0.17), residues: 894 sheet: 0.76 (0.61), residues: 74 loop : -1.09 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2814 TYR 0.015 0.001 TYR A1054 PHE 0.032 0.001 PHE A3142 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11964) covalent geometry : angle 0.48037 / 0.25 (16246) hydrogen bonds : bond 0.03517 / 2.36 ( 699) hydrogen bonds : angle 3.83579 / 2.83 ( 2022) metal coordination : bond 0.00591 / 0.42 ( 6) metal coordination : angle 1.94031 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.475 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6444 (tp) REVERT: A 2462 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6243 (mp) REVERT: A 3011 HIS cc_start: 0.8102 (m-70) cc_final: 0.7850 (m-70) outliers start: 32 outliers final: 22 residues processed: 145 average time/residue: 0.1018 time to fit residues: 21.9329 Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3203 MET Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [142, 0, 124, 103, 21, 18, 5, 116, 85, 70, 54] chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.0000 chunk 54 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094067 restraints weight = 17406.817| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.51 r_work: 0.2947 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11970 Z= 0.153 Angle : 0.483 7.899 16252 Z= 0.251 Chirality : 0.039 0.350 1933 Planarity : 0.003 0.061 2021 Dihedral : 8.553 153.338 1728 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 2.43 % Allowed : 21.41 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1463 helix: 2.17 (0.17), residues: 894 sheet: 0.52 (0.59), residues: 79 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1583 TYR 0.012 0.001 TYR A1054 PHE 0.024 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (11964) covalent geometry : angle 0.48175 / 0.25 (16246) hydrogen bonds : bond 0.03523 / 2.36 ( 699) hydrogen bonds : angle 3.82275 / 2.82 ( 2022) metal coordination : bond 0.00608 / 0.43 ( 6) metal coordination : angle 1.89704 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.445 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6445 (tp) REVERT: A 3112 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6310 (mp) REVERT: A 3211 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8119 (mp0) outliers start: 31 outliers final: 24 residues processed: 143 average time/residue: 0.1008 time to fit residues: 21.5183 Evaluate side-chains 141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3062 ASP Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3203 MET Chi-restraints excluded: chain A residue 3211 GLU Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [47, 91, 49, 101, 87, 33, 36, 53, 46, 43, 57] chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1034 ASN A2618 GLN A2770 GLN A3043 GLN A3201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096802 restraints weight = 17272.185| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.48 r_work: 0.2999 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11970 Z= 0.101 Angle : 0.455 7.804 16252 Z= 0.238 Chirality : 0.038 0.330 1933 Planarity : 0.003 0.059 2021 Dihedral : 8.480 152.287 1728 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 1.25 % Allowed : 22.59 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1463 helix: 2.27 (0.18), residues: 895 sheet: 0.56 (0.58), residues: 79 loop : -1.09 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2750 TYR 0.014 0.001 TYR A1054 PHE 0.019 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.000 HIS A1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11964) covalent geometry : angle 0.45435 / 0.24 (16246) hydrogen bonds : bond 0.03158 / 2.12 ( 699) hydrogen bonds : angle 3.69887 / 2.73 ( 2022) metal coordination : bond 0.00343 / 0.25 ( 6) metal coordination : angle 1.70895 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.419 Fit side-chains REVERT: A 1144 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6502 (tp) REVERT: A 3112 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6264 (mp) outliers start: 16 outliers final: 12 residues processed: 142 average time/residue: 0.1047 time to fit residues: 21.7197 Evaluate side-chains 137 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3062 ASP Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [55, 112, 66, 146, 94, 76, 148, 7, 62, 22, 9] chunk 55 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096176 restraints weight = 17264.166| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.50 r_work: 0.2991 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11970 Z= 0.114 Angle : 0.473 8.910 16252 Z= 0.244 Chirality : 0.038 0.277 1933 Planarity : 0.003 0.059 2021 Dihedral : 8.472 152.090 1728 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 1.73 % Allowed : 22.51 % Favored : 75.76 % 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: 1.69 (0.22), residues: 1463 helix: 2.27 (0.18), residues: 894 sheet: 0.88 (0.60), residues: 74 loop : -1.07 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2815 TYR 0.013 0.001 TYR A1054 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.006 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (11964) covalent geometry : angle 0.47236 / 0.24 (16246) hydrogen bonds : bond 0.03199 / 2.15 ( 699) hydrogen bonds : angle 3.69825 / 2.73 ( 2022) metal coordination : bond 0.00390 / 0.28 ( 6) metal coordination : angle 1.70916 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.313 Fit side-chains REVERT: A 2770 GLN cc_start: 0.8589 (mm110) cc_final: 0.8303 (mm-40) REVERT: A 3112 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 22 outliers final: 15 residues processed: 142 average time/residue: 0.1022 time to fit residues: 21.5740 Evaluate side-chains 134 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3062 ASP Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [126, 137, 82, 71, 12, 144, 123, 26, 18, 13, 120] chunk 126 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095161 restraints weight = 17407.844| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.51 r_work: 0.2964 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11970 Z= 0.137 Angle : 0.490 12.508 16252 Z= 0.252 Chirality : 0.039 0.272 1933 Planarity : 0.003 0.059 2021 Dihedral : 8.481 152.187 1728 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.08 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 22.98 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1463 helix: 2.24 (0.17), residues: 894 sheet: 0.98 (0.60), residues: 74 loop : -1.09 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2750 TYR 0.013 0.001 TYR A1054 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.007 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11964) covalent geometry : angle 0.48911 / 0.25 (16246) hydrogen bonds : bond 0.03302 / 2.22 ( 699) hydrogen bonds : angle 3.73336 / 2.75 ( 2022) metal coordination : bond 0.00494 / 0.35 ( 6) metal coordination : angle 1.66223 / 1.20 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.477 Fit side-chains REVERT: A 2770 GLN cc_start: 0.8569 (mm110) cc_final: 0.8256 (mp10) REVERT: A 3112 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6251 (mp) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.1024 time to fit residues: 19.8318 Evaluate side-chains 132 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3203 MET Chi-restraints excluded: chain A residue 3213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [10, 66, 53, 44, 74, 76, 68, 11, 20, 33, 35] chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096453 restraints weight = 17325.398| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.47 r_work: 0.2995 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11970 Z= 0.112 Angle : 0.471 11.316 16252 Z= 0.243 Chirality : 0.038 0.255 1933 Planarity : 0.003 0.059 2021 Dihedral : 8.448 151.880 1728 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Rotamer: Outliers : 1.49 % Allowed : 22.90 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.22), residues: 1463 helix: 2.26 (0.17), residues: 896 sheet: 0.75 (0.58), residues: 79 loop : -1.07 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2815 TYR 0.014 0.001 TYR A1054 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.006 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (11964) covalent geometry : angle 0.47020 / 0.24 (16246) hydrogen bonds : bond 0.03173 / 2.13 ( 699) hydrogen bonds : angle 3.67232 / 2.72 ( 2022) metal coordination : bond 0.00379 / 0.28 ( 6) metal coordination : angle 1.59638 / 1.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2781.59 seconds wall clock time: 48 minutes 38.70 seconds (2918.70 seconds total)