Starting phenix.real_space_refine on Sat Oct 24 10:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.cif Found real_map, /net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.map" model { file = "/net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26jz_80706/10_2026/26jz_80706.cif" } resolution = 2.65 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= 0.001 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 18 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 7957 2.51 5 N 2170 2.21 5 O 2436 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: 12674 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1571, 12289 Classifications: {'peptide': 1571} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 48, 'TRANS': 1522} Chain breaks: 11 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 21, 'ARG:plan': 10, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 157 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: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 5} 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 41.766 17.017 93.206 1.00 81.66 S ATOM 822 SG CYS A1031 44.743 14.704 93.351 1.00 88.30 S ATOM 1065 SG CYS A1062 41.438 13.363 92.062 1.00 87.91 S ATOM 1085 SG CYS A1065 43.342 15.861 89.971 1.00 92.16 S ATOM 2539 SG CYS A1294 54.716 25.800 42.496 1.00 60.27 S Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12674 At special positions: 0 Unit cell: (112.42, 105.85, 125.56, 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 89 16.00 P 18 15.00 Mg 1 11.99 O 2436 8.00 N 2170 7.00 C 7957 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 580.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " 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 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 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 11 sheets defined 62.9% alpha, 6.8% beta 1 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.647A pdb=" N VAL A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.663A 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: 3.631A 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: 3.972A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1112 Processing helix chain 'A' and resid 1118 through 1140 removed outlier: 3.590A pdb=" N GLY A1140 " --> pdb=" O MET A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.552A pdb=" N SER A1190 " --> pdb=" O GLU A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1234 removed outlier: 3.774A pdb=" N LEU A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A1234 " --> pdb=" O PHE A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 Processing helix chain 'A' and resid 1279 through 1282 removed outlier: 3.518A pdb=" N LYS A1282 " --> pdb=" O PHE A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1291 through 1295 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: 4.287A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1435 Processing helix chain 'A' and resid 1436 through 1463 Processing helix chain 'A' and resid 1465 through 1481 Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 4.065A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1531 removed outlier: 4.180A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.271A 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: 3.847A 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: 4.111A 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: 3.667A pdb=" N GLU A1634 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 3.502A 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 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 2295 through 2306 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: 3.842A pdb=" N ILE A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2440 Processing helix chain 'A' and resid 2441 through 2444 Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.897A pdb=" N LYS A2451 " --> pdb=" O ASN A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.961A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2559 removed outlier: 4.942A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.546A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.587A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2595 through 2600' Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.827A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.619A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.334A 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: 3.626A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.510A pdb=" N ASN A2697 " --> pdb=" O THR A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2701 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 2898 through 2912 Processing helix chain 'A' and resid 2944 through 2954 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: 3.667A pdb=" N ILE A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) removed outlier: 3.686A 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 3163 Processing helix chain 'A' and resid 3167 through 3172 Processing helix chain 'A' and resid 3174 through 3185 Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.772A 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: 6.817A 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: 4.124A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (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: 4.481A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2956 through 2960 removed outlier: 4.269A pdb=" N ILE A2990 " --> pdb=" O ASP A2960 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.560A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3076 through 3081 removed outlier: 4.090A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3089 723 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2940 1.33 - 1.45: 2617 1.45 - 1.57: 7206 1.57 - 1.69: 34 1.69 - 1.81: 128 Bond restraints: 12925 Sorted by residual: bond pdb=" N ILE A1085 " pdb=" CA ILE A1085 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.05e+00 bond pdb=" N VAL A1078 " pdb=" CA VAL A1078 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.39e+00 bond pdb=" N SER A1076 " pdb=" CA SER A1076 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.62e+00 bond pdb=" N ASN A1077 " pdb=" CA ASN A1077 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.21e-02 6.83e+03 6.35e+00 bond pdb=" P U B 10 " pdb=" O5' U B 10 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.69e+00 ... (remaining 12920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17281 2.10 - 4.20: 243 4.20 - 6.31: 37 6.31 - 8.41: 1 8.41 - 10.51: 3 Bond angle restraints: 17565 Sorted by residual: angle pdb=" C5 G C 23 " pdb=" C4 G C 23 " pdb=" N3 G C 23 " ideal model delta sigma weight residual 128.60 126.38 2.22 5.00e-01 4.00e+00 1.97e+01 angle pdb=" O4' C B 4 " pdb=" C1' C B 4 " pdb=" N1 C B 4 " ideal model delta sigma weight residual 108.50 111.59 -3.09 7.00e-01 2.04e+00 1.95e+01 angle pdb=" C1' G C 23 " pdb=" N9 G C 23 " pdb=" C4 G C 23 " ideal model delta sigma weight residual 126.50 132.11 -5.61 1.30e+00 5.92e-01 1.86e+01 angle pdb=" N9 G C 23 " pdb=" C4 G C 23 " pdb=" N3 G C 23 " ideal model delta sigma weight residual 126.00 128.52 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" O5' A C 24 " pdb=" C5' A C 24 " pdb=" C4' A C 24 " ideal model delta sigma weight residual 109.40 112.73 -3.33 8.00e-01 1.56e+00 1.74e+01 ... (remaining 17560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 7510 33.88 - 67.76: 340 67.76 - 101.64: 21 101.64 - 135.52: 1 135.52 - 169.40: 1 Dihedral angle restraints: 7873 sinusoidal: 3257 harmonic: 4616 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 30.60 169.40 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" C5' U B 10 " pdb=" C4' U B 10 " pdb=" C3' U B 10 " pdb=" O3' U B 10 " ideal model delta sinusoidal sigma weight residual 147.00 88.09 58.91 1 8.00e+00 1.56e-02 7.25e+01 dihedral pdb=" O4' U B 10 " pdb=" C4' U B 10 " pdb=" C3' U B 10 " pdb=" C2' U B 10 " ideal model delta sinusoidal sigma weight residual 24.00 -32.18 56.18 1 8.00e+00 1.56e-02 6.65e+01 ... (remaining 7870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1997 0.103 - 0.206: 64 0.206 - 0.310: 0 0.310 - 0.413: 0 0.413 - 0.516: 6 Chirality restraints: 2067 Sorted by residual: chirality pdb=" P A B 9 " pdb=" OP1 A B 9 " pdb=" OP2 A B 9 " pdb=" O5' A B 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.66e+00 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 -2.92 -0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" P U B 3 " pdb=" OP1 U B 3 " pdb=" OP2 U B 3 " pdb=" O5' U B 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2064 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1286 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A1287 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1287 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1287 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2362 " -0.011 2.00e-02 2.50e+03 1.07e-02 2.85e+00 pdb=" CG TRP A2362 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A2362 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A2362 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2362 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2362 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2362 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2362 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2362 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A2362 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1041 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" CD GLU A1041 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A1041 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A1041 " -0.010 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 97 2.58 - 3.16: 10630 3.16 - 3.74: 21095 3.74 - 4.32: 28750 4.32 - 4.90: 47932 Nonbonded interactions: 108504 Sorted by model distance: nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.004 2.230 nonbonded pdb=" OE2 GLU A2575 " pdb="MN MN A4003 " model vdw 2.077 2.320 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.099 2.320 nonbonded pdb=" OD2 ASP A2518 " pdb="MN MN A4003 " model vdw 2.113 2.320 nonbonded pdb=" CD2 HIS A1365 " pdb="ZN ZN A4002 " model vdw 2.142 2.450 ... (remaining 108499 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: 4.800 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.004 0.043 12931 Z= 0.205 Angle : 0.600 10.511 17571 Z= 0.348 Chirality : 0.049 0.516 2067 Planarity : 0.003 0.048 2163 Dihedral : 17.673 169.395 4863 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 0.07 % Allowed : 23.84 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1547 helix: 2.16 (0.18), residues: 894 sheet: 1.86 (0.66), residues: 59 loop : -0.88 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1348 TYR 0.012 0.001 TYR A1503 PHE 0.020 0.001 PHE A2633 TRP 0.029 0.001 TRP A2362 HIS 0.002 0.001 HIS A2477 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (12925) covalent geometry : angle 0.59928 / 0.35 (17565) hydrogen bonds : bond 0.10682 / 7.33 ( 726) hydrogen bonds : angle 4.59934 / 3.30 ( 2094) metal coordination : bond 0.00434 / 0.29 ( 6) metal coordination : angle 1.25823 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.354 Fit side-chains REVERT: A 1348 ARG cc_start: 0.8028 (ttt90) cc_final: 0.7609 (ttm170) REVERT: A 2682 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 3020 PHE cc_start: 0.9012 (m-10) cc_final: 0.8808 (m-80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.5289 time to fit residues: 83.9124 Evaluate side-chains 133 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092857 restraints weight = 18321.254| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.50 r_work: 0.3011 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12931 Z= 0.176 Angle : 0.533 8.467 17571 Z= 0.276 Chirality : 0.040 0.176 2067 Planarity : 0.003 0.057 2163 Dihedral : 10.926 162.603 1946 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 2.32 % Allowed : 21.52 % 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: 1.43 (0.22), residues: 1547 helix: 2.05 (0.18), residues: 903 sheet: 1.77 (0.66), residues: 59 loop : -0.96 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1348 TYR 0.010 0.001 TYR A1503 PHE 0.022 0.001 PHE A2633 TRP 0.015 0.001 TRP A2362 HIS 0.004 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (12925) covalent geometry : angle 0.53125 / 0.28 (17565) hydrogen bonds : bond 0.04060 / 2.70 ( 726) hydrogen bonds : angle 4.10714 / 2.99 ( 2094) metal coordination : bond 0.00584 / 0.39 ( 6) metal coordination : angle 2.28716 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 1798 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: A 2646 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 2682 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 3127 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (p0) outliers start: 32 outliers final: 11 residues processed: 153 average time/residue: 0.4818 time to fit residues: 81.4775 Evaluate side-chains 140 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 2899 LEU Chi-restraints excluded: chain A residue 3127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [139, 142, 15, 84, 10, 71, 35, 150, 17, 130, 80] chunk 139 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092976 restraints weight = 18513.057| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.52 r_work: 0.3051 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12931 Z= 0.149 Angle : 0.506 9.049 17571 Z= 0.262 Chirality : 0.039 0.170 2067 Planarity : 0.003 0.058 2163 Dihedral : 10.766 158.141 1946 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 2.75 % Allowed : 21.96 % 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: 1.41 (0.22), residues: 1547 helix: 2.07 (0.17), residues: 903 sheet: 1.75 (0.67), residues: 59 loop : -1.02 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1111 TYR 0.014 0.001 TYR A1054 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A2477 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (12925) covalent geometry : angle 0.50545 / 0.26 (17565) hydrogen bonds : bond 0.03757 / 2.51 ( 726) hydrogen bonds : angle 3.99358 / 2.92 ( 2094) metal coordination : bond 0.00520 / 0.35 ( 6) metal coordination : angle 1.61843 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: A 960 GLN cc_start: 0.8266 (mt0) cc_final: 0.8015 (mt0) REVERT: A 1547 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 2579 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 2646 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: A 2682 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 3127 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8122 (p0) REVERT: A 3137 LYS cc_start: 0.7837 (mttt) cc_final: 0.7625 (mttt) REVERT: A 3211 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (mp0) outliers start: 38 outliers final: 14 residues processed: 159 average time/residue: 0.5067 time to fit residues: 88.7630 Evaluate side-chains 145 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1800 ILE Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [63, 113, 28, 143, 153, 48, 26, 91, 34, 110, 57] chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092395 restraints weight = 18383.164| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.51 r_work: 0.3007 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12931 Z= 0.152 Angle : 0.509 9.368 17571 Z= 0.261 Chirality : 0.039 0.168 2067 Planarity : 0.003 0.057 2163 Dihedral : 10.691 155.438 1946 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 22.46 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1547 helix: 2.09 (0.17), residues: 903 sheet: 1.74 (0.67), residues: 59 loop : -1.01 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1108 TYR 0.010 0.001 TYR A1054 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.008 0.001 HIS A2644 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (12925) covalent geometry : angle 0.50815 / 0.26 (17565) hydrogen bonds : bond 0.03636 / 2.43 ( 726) hydrogen bonds : angle 3.95423 / 2.90 ( 2094) metal coordination : bond 0.00523 / 0.35 ( 6) metal coordination : angle 1.56477 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 960 GLN cc_start: 0.8267 (mt0) cc_final: 0.7965 (mt0) REVERT: A 1459 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 1547 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 2579 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7932 (mt-10) REVERT: A 2646 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: A 2682 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 3127 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (p0) REVERT: A 3137 LYS cc_start: 0.7833 (mttt) cc_final: 0.7625 (mttt) REVERT: A 3211 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7983 (mp0) outliers start: 38 outliers final: 11 residues processed: 160 average time/residue: 0.4847 time to fit residues: 85.8524 Evaluate side-chains 143 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [49, 44, 149, 16, 104, 87, 2, 45, 126, 15, 150] chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093043 restraints weight = 18413.225| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.51 r_work: 0.3053 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12931 Z= 0.134 Angle : 0.505 9.529 17571 Z= 0.258 Chirality : 0.039 0.164 2067 Planarity : 0.003 0.057 2163 Dihedral : 10.621 154.309 1946 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.54 % Allowed : 23.04 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.22), residues: 1547 helix: 2.12 (0.17), residues: 903 sheet: 1.67 (0.66), residues: 59 loop : -0.98 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1108 TYR 0.014 0.001 TYR A1054 PHE 0.020 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A2644 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12925) covalent geometry : angle 0.50441 / 0.26 (17565) hydrogen bonds : bond 0.03503 / 2.35 ( 726) hydrogen bonds : angle 3.89949 / 2.86 ( 2094) metal coordination : bond 0.00477 / 0.33 ( 6) metal coordination : angle 1.42466 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.405 Fit side-chains REVERT: A 960 GLN cc_start: 0.8337 (mt0) cc_final: 0.8005 (mt0) REVERT: A 975 GLU cc_start: 0.8311 (tp30) cc_final: 0.8060 (tp30) REVERT: A 1217 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5563 (mttt) REVERT: A 1432 ILE cc_start: 0.8910 (mm) cc_final: 0.8695 (OUTLIER) REVERT: A 1459 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8173 (p) REVERT: A 1547 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 2646 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 2682 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 3127 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8124 (p0) REVERT: A 3211 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7923 (mp0) outliers start: 35 outliers final: 14 residues processed: 156 average time/residue: 0.5021 time to fit residues: 86.4651 Evaluate side-chains 143 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [77, 118, 28, 83, 48, 135, 85, 30, 15, 99, 79] chunk 77 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 135 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090609 restraints weight = 18450.744| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.57 r_work: 0.3041 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12931 Z= 0.133 Angle : 0.503 9.568 17571 Z= 0.256 Chirality : 0.038 0.163 2067 Planarity : 0.003 0.056 2163 Dihedral : 10.574 153.684 1946 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 23.12 % Favored : 74.13 % 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: 1.53 (0.22), residues: 1547 helix: 2.16 (0.17), residues: 903 sheet: 1.69 (0.66), residues: 59 loop : -0.94 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1348 TYR 0.011 0.001 TYR A1054 PHE 0.021 0.001 PHE A2744 TRP 0.014 0.001 TRP A2542 HIS 0.007 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12925) covalent geometry : angle 0.50251 / 0.26 (17565) hydrogen bonds : bond 0.03463 / 2.33 ( 726) hydrogen bonds : angle 3.87793 / 2.84 ( 2094) metal coordination : bond 0.00461 / 0.32 ( 6) metal coordination : angle 1.44821 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 960 GLN cc_start: 0.8367 (mt0) cc_final: 0.8020 (mt0) REVERT: A 975 GLU cc_start: 0.8300 (tp30) cc_final: 0.8080 (tp30) REVERT: A 1217 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5670 (mttt) REVERT: A 1269 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 1459 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 1547 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 2646 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 2682 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 3127 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8130 (p0) REVERT: A 3211 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (mp0) outliers start: 38 outliers final: 18 residues processed: 160 average time/residue: 0.4992 time to fit residues: 88.4410 Evaluate side-chains 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2681 LEU Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2786 SER Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [102, 137, 123, 92, 129, 24, 66, 38, 107, 36, 3] chunk 102 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN A2996 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086351 restraints weight = 18571.985| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.58 r_work: 0.2969 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12931 Z= 0.251 Angle : 0.596 10.196 17571 Z= 0.303 Chirality : 0.042 0.172 2067 Planarity : 0.004 0.061 2163 Dihedral : 10.659 154.504 1946 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 3.12 % Allowed : 23.12 % Favored : 73.77 % 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: 1.32 (0.22), residues: 1547 helix: 1.98 (0.17), residues: 898 sheet: 1.60 (0.66), residues: 59 loop : -0.97 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1348 TYR 0.015 0.002 TYR A1612 PHE 0.029 0.002 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.013 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (12925) covalent geometry : angle 0.59521 / 0.30 (17565) hydrogen bonds : bond 0.04219 / 2.83 ( 726) hydrogen bonds : angle 4.11485 / 3.02 ( 2094) metal coordination : bond 0.00866 / 0.57 ( 6) metal coordination : angle 1.44326 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 975 GLU cc_start: 0.8328 (tp30) cc_final: 0.8120 (tp30) REVERT: A 1217 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5837 (mttt) REVERT: A 1459 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 1547 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8890 (p) REVERT: A 2561 MET cc_start: 0.8893 (mtm) cc_final: 0.8679 (mtp) REVERT: A 2646 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 2682 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 3127 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8104 (p0) REVERT: A 3211 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8025 (mp0) outliers start: 43 outliers final: 17 residues processed: 158 average time/residue: 0.4870 time to fit residues: 85.4580 Evaluate side-chains 146 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2604 THR Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2786 SER Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [108, 102, 51, 79, 21, 68, 112, 70, 71, 113, 12] chunk 108 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089714 restraints weight = 18305.143| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.58 r_work: 0.3022 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12931 Z= 0.127 Angle : 0.527 8.832 17571 Z= 0.269 Chirality : 0.039 0.164 2067 Planarity : 0.004 0.061 2163 Dihedral : 10.579 153.851 1946 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 1.74 % Allowed : 24.49 % Favored : 73.77 % 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: 1.47 (0.22), residues: 1547 helix: 2.11 (0.17), residues: 897 sheet: 1.58 (0.65), residues: 59 loop : -0.92 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1108 TYR 0.013 0.001 TYR A1054 PHE 0.018 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.011 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12925) covalent geometry : angle 0.52612 / 0.27 (17565) hydrogen bonds : bond 0.03548 / 2.39 ( 726) hydrogen bonds : angle 3.94684 / 2.90 ( 2094) metal coordination : bond 0.00430 / 0.30 ( 6) metal coordination : angle 1.37942 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.469 Fit side-chains REVERT: A 975 GLU cc_start: 0.8315 (tp30) cc_final: 0.8100 (tp30) REVERT: A 1217 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5753 (mttt) REVERT: A 1348 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7349 (ttm170) REVERT: A 1459 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8114 (p) REVERT: A 1547 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8801 (p) REVERT: A 1806 ASP cc_start: 0.8124 (t70) cc_final: 0.7627 (t0) REVERT: A 2646 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 2682 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 3127 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8138 (p0) outliers start: 24 outliers final: 11 residues processed: 145 average time/residue: 0.4916 time to fit residues: 78.6612 Evaluate side-chains 138 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 3127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [48, 10, 127, 63, 111, 5, 123, 85, 104, 41, 28] chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088274 restraints weight = 18480.028| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.56 r_work: 0.2999 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12931 Z= 0.184 Angle : 0.550 9.121 17571 Z= 0.279 Chirality : 0.040 0.171 2067 Planarity : 0.004 0.060 2163 Dihedral : 10.599 154.419 1946 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.23 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 24.49 % Favored : 73.48 % 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: 1.41 (0.22), residues: 1547 helix: 2.07 (0.17), residues: 898 sheet: 1.48 (0.65), residues: 59 loop : -0.96 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1108 TYR 0.011 0.001 TYR A1054 PHE 0.024 0.002 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.011 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (12925) covalent geometry : angle 0.54957 / 0.28 (17565) hydrogen bonds : bond 0.03767 / 2.53 ( 726) hydrogen bonds : angle 3.98876 / 2.93 ( 2094) metal coordination : bond 0.00651 / 0.44 ( 6) metal coordination : angle 1.42040 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 1217 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5765 (mttt) REVERT: A 1459 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8096 (p) REVERT: A 1547 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 1801 ASP cc_start: 0.8505 (t0) cc_final: 0.8109 (p0) REVERT: A 1806 ASP cc_start: 0.8130 (t70) cc_final: 0.7511 (t0) REVERT: A 2561 MET cc_start: 0.8838 (mtm) cc_final: 0.8593 (mtp) REVERT: A 2646 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 2682 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 3127 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8135 (p0) REVERT: A 3198 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7835 (tt) outliers start: 28 outliers final: 12 residues processed: 142 average time/residue: 0.4851 time to fit residues: 76.3422 Evaluate side-chains 138 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2786 SER Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [91, 144, 112, 21, 146, 20, 111, 13, 14, 124, 103] chunk 91 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089198 restraints weight = 18563.424| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.58 r_work: 0.3012 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12931 Z= 0.148 Angle : 0.533 8.832 17571 Z= 0.272 Chirality : 0.039 0.166 2067 Planarity : 0.003 0.060 2163 Dihedral : 10.570 153.841 1946 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 1.67 % Allowed : 24.93 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1547 helix: 2.09 (0.17), residues: 897 sheet: 1.46 (0.65), residues: 59 loop : -0.93 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1108 TYR 0.011 0.001 TYR A1054 PHE 0.022 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.011 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12925) covalent geometry : angle 0.53248 / 0.27 (17565) hydrogen bonds : bond 0.03598 / 2.42 ( 726) hydrogen bonds : angle 3.95295 / 2.91 ( 2094) metal coordination : bond 0.00518 / 0.36 ( 6) metal coordination : angle 1.40831 / 0.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.500 Fit side-chains REVERT: A 1217 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5745 (mttt) REVERT: A 1348 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7723 (ttm170) REVERT: A 1432 ILE cc_start: 0.8884 (mm) cc_final: 0.8657 (OUTLIER) REVERT: A 1459 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 1547 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 1801 ASP cc_start: 0.8547 (t0) cc_final: 0.8146 (p0) REVERT: A 1806 ASP cc_start: 0.8141 (t70) cc_final: 0.7648 (t0) REVERT: A 2646 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 2682 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 3127 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8113 (p0) REVERT: A 3198 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 3211 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8016 (mp0) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.5049 time to fit residues: 77.0766 Evaluate side-chains 138 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2602 SER Chi-restraints excluded: chain A residue 2646 GLU Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2749 ASN Chi-restraints excluded: chain A residue 2766 LEU Chi-restraints excluded: chain A residue 2786 SER Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3127 ASP Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [26, 22, 85, 41, 156, 155, 82, 104, 91, 105, 66] chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090288 restraints weight = 18413.274| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.58 r_work: 0.3032 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 0.003 0.042 12931 Z= 0.128 Angle : 0.528 10.967 17571 Z= 0.268 Chirality : 0.039 0.211 2067 Planarity : 0.003 0.059 2163 Dihedral : 10.537 153.215 1946 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 1.67 % Allowed : 24.71 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1547 helix: 2.13 (0.17), residues: 897 sheet: 1.39 (0.66), residues: 59 loop : -0.93 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1108 TYR 0.011 0.001 TYR A1054 PHE 0.020 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.012 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12925) covalent geometry : angle 0.52741 / 0.27 (17565) hydrogen bonds : bond 0.03431 / 2.31 ( 726) hydrogen bonds : angle 3.89803 / 2.87 ( 2094) metal coordination : bond 0.00453 / 0.31 ( 6) metal coordination : angle 1.42127 / 0.78 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.71 seconds wall clock time: 70 minutes 39.66 seconds (4239.66 seconds total)