Starting phenix.real_space_refine on Tue Aug 26 10:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.map" model { file = "/net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s24_19653/08_2025/8s24_19653.cif" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 213 5.16 5 C 22585 2.51 5 N 6086 2.21 5 O 6468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35357 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 35324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4387, 35324 Classifications: {'peptide': 4387} Link IDs: {'PCIS': 4, 'PTRANS': 172, 'TRANS': 4210} Chain breaks: 39 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 30218 SG CYS A4505 67.192 89.943 142.255 1.00124.47 S ATOM 30294 SG CYS A4528 66.168 84.998 141.218 1.00120.36 S Time building chain proxies: 8.08, per 1000 atoms: 0.23 Number of scatterers: 35357 At special positions: 0 Unit cell: (130.782, 152.886, 231.171, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 213 16.00 P 3 15.00 Mg 1 11.99 O 6468 8.00 N 6086 7.00 C 22585 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: 3.09 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5303 " pdb="ZN ZN A5303 " - pdb=" SG CYS A4505 " pdb="ZN ZN A5303 " - pdb=" SG CYS A4528 " 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 20 sheets defined 64.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 545 through 565 removed outlier: 3.832A pdb=" N GLN A 565 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 599 Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 640 through 648 removed outlier: 4.066A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 667 removed outlier: 4.324A pdb=" N HIS A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 665 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.569A pdb=" N ARG A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.551A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 727 through 734 Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.720A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 removed outlier: 4.553A pdb=" N ARG A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 777 removed outlier: 3.614A pdb=" N PHE A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 784 Processing helix chain 'A' and resid 785 through 797 removed outlier: 4.220A pdb=" N LEU A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 810 through 831 Processing helix chain 'A' and resid 842 through 859 removed outlier: 3.519A pdb=" N THR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 881 Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 934 through 944 Processing helix chain 'A' and resid 952 through 967 Processing helix chain 'A' and resid 969 through 980 Processing helix chain 'A' and resid 989 through 1009 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.576A pdb=" N PHE A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1054 Processing helix chain 'A' and resid 1055 through 1067 Processing helix chain 'A' and resid 1068 through 1073 removed outlier: 3.833A pdb=" N ALA A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1068 through 1073' Processing helix chain 'A' and resid 1075 through 1099 Processing helix chain 'A' and resid 1102 through 1112 Processing helix chain 'A' and resid 1112 through 1125 Processing helix chain 'A' and resid 1136 through 1165 Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1185 through 1189 removed outlier: 3.833A pdb=" N SER A1188 " --> pdb=" O ASP A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1214 through 1227 Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1273 through 1278 Processing helix chain 'A' and resid 1278 through 1296 Processing helix chain 'A' and resid 1299 through 1308 removed outlier: 3.508A pdb=" N ILE A1303 " --> pdb=" O THR A1299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1308 " --> pdb=" O ASP A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1311 No H-bonds generated for 'chain 'A' and resid 1309 through 1311' Processing helix chain 'A' and resid 1313 through 1323 Processing helix chain 'A' and resid 1324 through 1327 removed outlier: 4.465A pdb=" N VAL A1327 " --> pdb=" O MET A1324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1324 through 1327' Processing helix chain 'A' and resid 1340 through 1366 Processing helix chain 'A' and resid 1372 through 1374 No H-bonds generated for 'chain 'A' and resid 1372 through 1374' Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1384 through 1390 removed outlier: 4.420A pdb=" N ARG A1390 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1407 removed outlier: 3.947A pdb=" N GLN A1402 " --> pdb=" O GLN A1398 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1403 " --> pdb=" O GLU A1399 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A1405 " --> pdb=" O ILE A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1424 removed outlier: 3.875A pdb=" N ARG A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1435 Processing helix chain 'A' and resid 1438 through 1451 removed outlier: 4.128A pdb=" N LYS A1442 " --> pdb=" O ILE A1438 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A1443 " --> pdb=" O ASN A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 4.543A pdb=" N VAL A1462 " --> pdb=" O ASP A1458 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A1463 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A1465 " --> pdb=" O ARG A1461 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A1468 " --> pdb=" O CYS A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1477 Processing helix chain 'A' and resid 1484 through 1502 removed outlier: 4.596A pdb=" N LYS A1494 " --> pdb=" O LYS A1490 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1495 " --> pdb=" O HIS A1491 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 Processing helix chain 'A' and resid 1515 through 1525 Processing helix chain 'A' and resid 1532 through 1544 Processing helix chain 'A' and resid 1558 through 1562 Processing helix chain 'A' and resid 1581 through 1595 Processing helix chain 'A' and resid 1603 through 1629 Processing helix chain 'A' and resid 1632 through 1637 removed outlier: 4.175A pdb=" N THR A1636 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1698 Processing helix chain 'A' and resid 1699 through 1704 removed outlier: 3.516A pdb=" N TYR A1704 " --> pdb=" O LEU A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1717 removed outlier: 4.288A pdb=" N ARG A1717 " --> pdb=" O SER A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 removed outlier: 3.609A pdb=" N PHE A1731 " --> pdb=" O THR A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1746 Processing helix chain 'A' and resid 1750 through 1770 Proline residue: A1765 - end of helix Processing helix chain 'A' and resid 1773 through 1788 Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 4.438A pdb=" N PHE A1792 " --> pdb=" O CYS A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1813 Processing helix chain 'A' and resid 1836 through 1850 removed outlier: 4.369A pdb=" N LEU A1841 " --> pdb=" O HIS A1837 " (cutoff:3.500A) Proline residue: A1842 - end of helix removed outlier: 3.613A pdb=" N GLN A1850 " --> pdb=" O ALA A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1870 through 1883 removed outlier: 3.658A pdb=" N VAL A1874 " --> pdb=" O THR A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1901 through 1918 Processing helix chain 'A' and resid 1933 through 1935 No H-bonds generated for 'chain 'A' and resid 1933 through 1935' Processing helix chain 'A' and resid 1937 through 1943 Processing helix chain 'A' and resid 1955 through 1968 Processing helix chain 'A' and resid 1975 through 1980 removed outlier: 3.913A pdb=" N VAL A1979 " --> pdb=" O ALA A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2013 Processing helix chain 'A' and resid 2031 through 2040 removed outlier: 3.571A pdb=" N VAL A2035 " --> pdb=" O ASP A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2044 removed outlier: 3.970A pdb=" N ASP A2044 " --> pdb=" O PRO A2041 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2041 through 2044' Processing helix chain 'A' and resid 2065 through 2075 Processing helix chain 'A' and resid 2122 through 2127 Processing helix chain 'A' and resid 2134 through 2142 removed outlier: 3.583A pdb=" N GLU A2142 " --> pdb=" O VAL A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2160 removed outlier: 3.564A pdb=" N PHE A2159 " --> pdb=" O ASP A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2176 Proline residue: A2167 - end of helix removed outlier: 3.514A pdb=" N GLN A2176 " --> pdb=" O ARG A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2193 through 2205 Processing helix chain 'A' and resid 2211 through 2231 Processing helix chain 'A' and resid 2246 through 2264 removed outlier: 3.936A pdb=" N PHE A2257 " --> pdb=" O THR A2253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A2264 " --> pdb=" O ARG A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2357 Processing helix chain 'A' and resid 2364 through 2368 Processing helix chain 'A' and resid 2369 through 2381 Processing helix chain 'A' and resid 2396 through 2413 Processing helix chain 'A' and resid 2425 through 2439 Processing helix chain 'A' and resid 2456 through 2478 Processing helix chain 'A' and resid 2488 through 2493 removed outlier: 3.636A pdb=" N THR A2492 " --> pdb=" O ALA A2489 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU A2493 " --> pdb=" O ASN A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2503 removed outlier: 3.688A pdb=" N ILE A2498 " --> pdb=" O ALA A2494 " (cutoff:3.500A) Processing helix chain 'A' and resid 2531 through 2540 Processing helix chain 'A' and resid 2562 through 2564 No H-bonds generated for 'chain 'A' and resid 2562 through 2564' Processing helix chain 'A' and resid 2586 through 2606 removed outlier: 3.897A pdb=" N SER A2604 " --> pdb=" O ARG A2600 " (cutoff:3.500A) Processing helix chain 'A' and resid 2608 through 2629 Processing helix chain 'A' and resid 2637 through 2654 removed outlier: 3.917A pdb=" N VAL A2641 " --> pdb=" O SER A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2669 Processing helix chain 'A' and resid 2679 through 2693 Processing helix chain 'A' and resid 2699 through 2709 removed outlier: 4.216A pdb=" N ARG A2709 " --> pdb=" O LYS A2705 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2734 Processing helix chain 'A' and resid 2745 through 2761 Processing helix chain 'A' and resid 2775 through 2786 Processing helix chain 'A' and resid 2787 through 2791 removed outlier: 4.003A pdb=" N ALA A2790 " --> pdb=" O GLN A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2799 removed outlier: 3.637A pdb=" N SER A2798 " --> pdb=" O LEU A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2814 through 2830 removed outlier: 3.766A pdb=" N ILE A2818 " --> pdb=" O THR A2814 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2850 Processing helix chain 'A' and resid 2856 through 2858 No H-bonds generated for 'chain 'A' and resid 2856 through 2858' Processing helix chain 'A' and resid 2859 through 2867 Processing helix chain 'A' and resid 2874 through 2878 Processing helix chain 'A' and resid 2890 through 2894 Processing helix chain 'A' and resid 2906 through 2918 Processing helix chain 'A' and resid 2921 through 2929 Processing helix chain 'A' and resid 2931 through 2946 Processing helix chain 'A' and resid 2952 through 2971 removed outlier: 3.525A pdb=" N TYR A2956 " --> pdb=" O GLY A2952 " (cutoff:3.500A) Processing helix chain 'A' and resid 2975 through 2987 Processing helix chain 'A' and resid 2996 through 3001 removed outlier: 3.629A pdb=" N ALA A3001 " --> pdb=" O ASP A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3013 through 3023 Processing helix chain 'A' and resid 3049 through 3059 removed outlier: 4.189A pdb=" N GLN A3053 " --> pdb=" O TYR A3049 " (cutoff:3.500A) Processing helix chain 'A' and resid 3079 through 3097 removed outlier: 4.076A pdb=" N LEU A3083 " --> pdb=" O GLU A3079 " (cutoff:3.500A) Processing helix chain 'A' and resid 3112 through 3117 removed outlier: 3.501A pdb=" N ASN A3117 " --> pdb=" O TYR A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3161 Processing helix chain 'A' and resid 3162 through 3168 Processing helix chain 'A' and resid 3175 through 3179 Processing helix chain 'A' and resid 3181 through 3200 removed outlier: 3.518A pdb=" N ASN A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3213 through 3218 Processing helix chain 'A' and resid 3224 through 3238 Processing helix chain 'A' and resid 3243 through 3260 Processing helix chain 'A' and resid 3263 through 3274 removed outlier: 3.569A pdb=" N VAL A3267 " --> pdb=" O THR A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3277 through 3289 Processing helix chain 'A' and resid 3295 through 3306 Processing helix chain 'A' and resid 3326 through 3337 Processing helix chain 'A' and resid 3350 through 3352 No H-bonds generated for 'chain 'A' and resid 3350 through 3352' Processing helix chain 'A' and resid 3354 through 3367 removed outlier: 3.557A pdb=" N PHE A3358 " --> pdb=" O THR A3354 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3405 Processing helix chain 'A' and resid 3457 through 3461 removed outlier: 3.766A pdb=" N VAL A3461 " --> pdb=" O LEU A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3531 through 3545 removed outlier: 5.253A pdb=" N GLN A3541 " --> pdb=" O ARG A3537 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER A3542 " --> pdb=" O SER A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3568 removed outlier: 3.655A pdb=" N ARG A3559 " --> pdb=" O THR A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3572 through 3596 removed outlier: 3.665A pdb=" N SER A3596 " --> pdb=" O LYS A3592 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3601 No H-bonds generated for 'chain 'A' and resid 3599 through 3601' Processing helix chain 'A' and resid 3602 through 3609 removed outlier: 3.733A pdb=" N ARG A3606 " --> pdb=" O GLU A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3610 through 3618 removed outlier: 3.733A pdb=" N LEU A3614 " --> pdb=" O ASN A3610 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3644 Proline residue: A3634 - end of helix Processing helix chain 'A' and resid 3647 through 3654 removed outlier: 4.142A pdb=" N LEU A3651 " --> pdb=" O GLY A3647 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A3652 " --> pdb=" O ASN A3648 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A3653 " --> pdb=" O LEU A3649 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3671 Processing helix chain 'A' and resid 3711 through 3730 Processing helix chain 'A' and resid 3734 through 3746 Processing helix chain 'A' and resid 3746 through 3753 Processing helix chain 'A' and resid 3757 through 3776 Processing helix chain 'A' and resid 3780 through 3801 Processing helix chain 'A' and resid 3810 through 3821 removed outlier: 4.052A pdb=" N VAL A3814 " --> pdb=" O SER A3810 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A3815 " --> pdb=" O LEU A3811 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3835 Processing helix chain 'A' and resid 3836 through 3842 removed outlier: 3.538A pdb=" N LEU A3842 " --> pdb=" O LEU A3839 " (cutoff:3.500A) Processing helix chain 'A' and resid 3857 through 3873 Processing helix chain 'A' and resid 3878 through 3889 Processing helix chain 'A' and resid 3889 through 3897 Processing helix chain 'A' and resid 3906 through 3934 removed outlier: 4.006A pdb=" N ARG A3922 " --> pdb=" O ALA A3918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3936 through 3941 Processing helix chain 'A' and resid 3944 through 3959 removed outlier: 4.039A pdb=" N PHE A3953 " --> pdb=" O THR A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3990 removed outlier: 5.791A pdb=" N SER A3986 " --> pdb=" O LYS A3982 " (cutoff:3.500A) Processing helix chain 'A' and resid 4017 through 4025 removed outlier: 4.000A pdb=" N LEU A4021 " --> pdb=" O CYS A4017 " (cutoff:3.500A) Processing helix chain 'A' and resid 4049 through 4076 Processing helix chain 'A' and resid 4085 through 4095 Processing helix chain 'A' and resid 4133 through 4139 Processing helix chain 'A' and resid 4142 through 4159 removed outlier: 3.709A pdb=" N VAL A4146 " --> pdb=" O SER A4142 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP A4148 " --> pdb=" O HIS A4144 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR A4149 " --> pdb=" O ASP A4145 " (cutoff:3.500A) Processing helix chain 'A' and resid 4167 through 4188 removed outlier: 4.151A pdb=" N ALA A4188 " --> pdb=" O GLU A4184 " (cutoff:3.500A) Processing helix chain 'A' and resid 4190 through 4208 Processing helix chain 'A' and resid 4222 through 4245 Processing helix chain 'A' and resid 4255 through 4270 Processing helix chain 'A' and resid 4272 through 4296 removed outlier: 4.245A pdb=" N ARG A4276 " --> pdb=" O ASN A4272 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N MET A4289 " --> pdb=" O SER A4285 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N GLU A4290 " --> pdb=" O GLN A4286 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A4291 " --> pdb=" O ARG A4287 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A4292 " --> pdb=" O GLY A4288 " (cutoff:3.500A) Processing helix chain 'A' and resid 4325 through 4330 Processing helix chain 'A' and resid 4331 through 4348 Processing helix chain 'A' and resid 4351 through 4360 Processing helix chain 'A' and resid 4363 through 4379 Processing helix chain 'A' and resid 4379 through 4385 removed outlier: 3.707A pdb=" N ARG A4384 " --> pdb=" O ALA A4380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A4385 " --> pdb=" O ILE A4381 " (cutoff:3.500A) Processing helix chain 'A' and resid 4393 through 4407 Processing helix chain 'A' and resid 4412 through 4424 Processing helix chain 'A' and resid 4441 through 4457 Processing helix chain 'A' and resid 4459 through 4461 No H-bonds generated for 'chain 'A' and resid 4459 through 4461' Processing helix chain 'A' and resid 4462 through 4471 Processing helix chain 'A' and resid 4472 through 4476 removed outlier: 3.513A pdb=" N ALA A4476 " --> pdb=" O ALA A4473 " (cutoff:3.500A) Processing helix chain 'A' and resid 4575 through 4597 Processing helix chain 'A' and resid 4597 through 4605 removed outlier: 3.790A pdb=" N LEU A4601 " --> pdb=" O SER A4597 " (cutoff:3.500A) Processing helix chain 'A' and resid 4611 through 4632 Processing helix chain 'A' and resid 4634 through 4652 Processing helix chain 'A' and resid 4670 through 4706 Proline residue: A4687 - end of helix removed outlier: 5.393A pdb=" N ASP A4693 " --> pdb=" O LEU A4689 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS A4694 " --> pdb=" O GLU A4690 " (cutoff:3.500A) Proline residue: A4697 - end of helix Processing helix chain 'A' and resid 4712 through 4720 Processing helix chain 'A' and resid 4721 through 4725 Processing helix chain 'A' and resid 4748 through 4759 Processing helix chain 'A' and resid 4760 through 4765 Processing helix chain 'A' and resid 4765 through 4774 Processing helix chain 'A' and resid 4774 through 4779 Processing helix chain 'A' and resid 4780 through 4782 No H-bonds generated for 'chain 'A' and resid 4780 through 4782' Processing helix chain 'A' and resid 4783 through 4798 Processing helix chain 'A' and resid 4809 through 4815 Processing helix chain 'A' and resid 4818 through 4839 Processing helix chain 'A' and resid 4839 through 4846 removed outlier: 3.635A pdb=" N LEU A4843 " --> pdb=" O LEU A4839 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A4845 " --> pdb=" O ARG A4841 " (cutoff:3.500A) Processing helix chain 'A' and resid 4854 through 4858 removed outlier: 3.810A pdb=" N SER A4857 " --> pdb=" O ASP A4854 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A4858 " --> pdb=" O TYR A4855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4854 through 4858' Processing helix chain 'A' and resid 4877 through 4903 removed outlier: 3.716A pdb=" N THR A4881 " --> pdb=" O GLY A4877 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4935 Processing helix chain 'A' and resid 4952 through 4961 Processing helix chain 'A' and resid 4986 through 4998 removed outlier: 3.581A pdb=" N LEU A4990 " --> pdb=" O ASN A4986 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5015 Processing helix chain 'A' and resid 5017 through 5038 Processing helix chain 'A' and resid 5045 through 5052 Processing helix chain 'A' and resid 5062 through 5067 removed outlier: 4.149A pdb=" N ALA A5066 " --> pdb=" O HIS A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5071 through 5073 No H-bonds generated for 'chain 'A' and resid 5071 through 5073' Processing helix chain 'A' and resid 5074 through 5093 Processing helix chain 'A' and resid 5102 through 5107 removed outlier: 3.895A pdb=" N ALA A5107 " --> pdb=" O ARG A5104 " (cutoff:3.500A) Processing helix chain 'A' and resid 5110 through 5123 Processing helix chain 'A' and resid 5125 through 5141 Processing helix chain 'A' and resid 5159 through 5169 removed outlier: 3.540A pdb=" N LYS A5169 " --> pdb=" O TYR A5165 " (cutoff:3.500A) Processing helix chain 'A' and resid 5175 through 5181 Processing helix chain 'A' and resid 5186 through 5188 No H-bonds generated for 'chain 'A' and resid 5186 through 5188' Processing helix chain 'A' and resid 5189 through 5205 Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 427 removed outlier: 8.054A pdb=" N HIS A 421 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 436 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 423 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU A 434 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASP A 425 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 432 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 380 " --> pdb=" O TRP A 492 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN A 494 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A 382 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 401 through 404 removed outlier: 3.612A pdb=" N PHE A 401 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 453 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1578 through 1580 removed outlier: 5.566A pdb=" N SER A1650 " --> pdb=" O TYR A1642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1862 through 1864 removed outlier: 6.436A pdb=" N LEU A1863 " --> pdb=" O LEU A1895 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A1892 " --> pdb=" O VAL A1927 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A1929 " --> pdb=" O TYR A1892 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU A1894 " --> pdb=" O VAL A1929 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASP A1931 " --> pdb=" O LEU A1894 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A1831 " --> pdb=" O LEU A1926 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A1948 " --> pdb=" O PRO A1830 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A1832 " --> pdb=" O VAL A1948 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2020 through 2025 removed outlier: 6.522A pdb=" N LYS A2021 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A2057 " --> pdb=" O LYS A2021 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A2023 " --> pdb=" O ASP A2057 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A2052 " --> pdb=" O LEU A2094 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE A2096 " --> pdb=" O VAL A2052 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A2054 " --> pdb=" O ILE A2096 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU A2098 " --> pdb=" O PHE A2054 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A2056 " --> pdb=" O GLU A2098 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LEU A2100 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A2058 " --> pdb=" O LEU A2100 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A1991 " --> pdb=" O ILE A2099 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A2130 " --> pdb=" O VAL A1986 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A1988 " --> pdb=" O VAL A2130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2078 through 2080 Processing sheet with id=AA7, first strand: chain 'A' and resid 2305 through 2308 Processing sheet with id=AA8, first strand: chain 'A' and resid 2321 through 2324 removed outlier: 7.321A pdb=" N VAL A2330 " --> pdb=" O ARG A2343 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG A2343 " --> pdb=" O VAL A2330 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A2332 " --> pdb=" O ILE A2341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2446 through 2450 removed outlier: 4.417A pdb=" N VAL A2416 " --> pdb=" O ILE A2520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2506 through 2507 Processing sheet with id=AB2, first strand: chain 'A' and resid 2555 through 2556 removed outlier: 3.788A pdb=" N ILE A2559 " --> pdb=" O LEU A2556 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2801 through 2808 removed outlier: 5.928A pdb=" N GLN A2801 " --> pdb=" O VAL A2838 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A2840 " --> pdb=" O GLN A2801 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS A2803 " --> pdb=" O VAL A2840 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A2842 " --> pdb=" O HIS A2803 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A2805 " --> pdb=" O VAL A2842 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP A2844 " --> pdb=" O VAL A2805 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE A2807 " --> pdb=" O ASP A2844 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A2766 " --> pdb=" O VAL A2900 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3067 through 3069 removed outlier: 6.329A pdb=" N VAL A3100 " --> pdb=" O ILE A3149 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A3151 " --> pdb=" O VAL A3100 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A3102 " --> pdb=" O ILE A3151 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLU A3153 " --> pdb=" O LEU A3102 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A3042 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU A3152 " --> pdb=" O LEU A3042 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A3044 " --> pdb=" O GLU A3152 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A3041 " --> pdb=" O GLU A3170 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS A3172 " --> pdb=" O TYR A3041 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU A3043 " --> pdb=" O HIS A3172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3121 through 3123 removed outlier: 3.563A pdb=" N GLN A3126 " --> pdb=" O LEU A3123 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS A3127 " --> pdb=" O VAL A3142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3345 through 3348 removed outlier: 6.466A pdb=" N THR A3345 " --> pdb=" O ILE A3376 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLN A3378 " --> pdb=" O THR A3345 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A3347 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASP A3380 " --> pdb=" O LEU A3347 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLN A3438 " --> pdb=" O ALA A3313 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A3315 " --> pdb=" O GLN A3438 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL A3440 " --> pdb=" O PHE A3315 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A3317 " --> pdb=" O VAL A3440 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3547 through 3549 removed outlier: 6.669A pdb=" N ARG A3548 " --> pdb=" O VAL A3695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 4008 through 4009 Processing sheet with id=AB9, first strand: chain 'A' and resid 4097 through 4099 Processing sheet with id=AC1, first strand: chain 'A' and resid 4130 through 4131 Processing sheet with id=AC2, first strand: chain 'A' and resid 4503 through 4504 1951 hydrogen bonds defined for protein. 5673 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: 12.19 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11302 1.33 - 1.45: 4630 1.45 - 1.57: 19833 1.57 - 1.69: 5 1.69 - 1.81: 310 Bond restraints: 36080 Sorted by residual: bond pdb=" C4 ATP A5301 " pdb=" C5 ATP A5301 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C5 ATP A5301 " pdb=" C6 ATP A5301 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" C4 ATP A5301 " pdb=" N9 ATP A5301 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" C8 ATP A5301 " pdb=" N7 ATP A5301 " ideal model delta sigma weight residual 1.310 1.360 -0.050 1.00e-02 1.00e+04 2.50e+01 bond pdb=" C5 ATP A5301 " pdb=" N7 ATP A5301 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.00e+01 ... (remaining 36075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 48748 4.02 - 8.04: 34 8.04 - 12.06: 1 12.06 - 16.08: 0 16.08 - 20.10: 2 Bond angle restraints: 48785 Sorted by residual: angle pdb=" PB ATP A5301 " pdb=" O3B ATP A5301 " pdb=" PG ATP A5301 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PA ATP A5301 " pdb=" O3A ATP A5301 " pdb=" PB ATP A5301 " ideal model delta sigma weight residual 136.83 119.97 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" C5 ATP A5301 " pdb=" C4 ATP A5301 " pdb=" N3 ATP A5301 " ideal model delta sigma weight residual 126.80 119.63 7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" N3 ATP A5301 " pdb=" C4 ATP A5301 " pdb=" N9 ATP A5301 " ideal model delta sigma weight residual 127.04 133.91 -6.87 1.15e+00 7.59e-01 3.59e+01 angle pdb=" N1 ATP A5301 " pdb=" C2 ATP A5301 " pdb=" N3 ATP A5301 " ideal model delta sigma weight residual 128.69 123.55 5.14 1.00e+00 1.00e+00 2.65e+01 ... (remaining 48780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19492 17.96 - 35.93: 1932 35.93 - 53.89: 415 53.89 - 71.85: 62 71.85 - 89.82: 21 Dihedral angle restraints: 21922 sinusoidal: 9041 harmonic: 12881 Sorted by residual: dihedral pdb=" CA CYS A3981 " pdb=" C CYS A3981 " pdb=" N LYS A3982 " pdb=" CA LYS A3982 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA THR A1392 " pdb=" C THR A1392 " pdb=" N LEU A1393 " pdb=" CA LEU A1393 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLU A1272 " pdb=" C GLU A1272 " pdb=" N GLU A1273 " pdb=" CA GLU A1273 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 21919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3801 0.034 - 0.068: 1317 0.068 - 0.103: 334 0.103 - 0.137: 82 0.137 - 0.171: 1 Chirality restraints: 5535 Sorted by residual: chirality pdb=" C2' ATP A5301 " pdb=" C1' ATP A5301 " pdb=" C3' ATP A5301 " pdb=" O2' ATP A5301 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE A1548 " pdb=" N ILE A1548 " pdb=" C ILE A1548 " pdb=" CB ILE A1548 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A2383 " pdb=" N ILE A2383 " pdb=" C ILE A2383 " pdb=" CB ILE A2383 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 5532 not shown) Planarity restraints: 6189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1465 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE A1465 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE A1465 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS A1466 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A3983 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLU A3983 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU A3983 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A3984 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A3758 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A3759 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A3759 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A3759 " 0.022 5.00e-02 4.00e+02 ... (remaining 6186 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 247 2.45 - 3.06: 26068 3.06 - 3.68: 54560 3.68 - 4.29: 82946 4.29 - 4.90: 136987 Nonbonded interactions: 300808 Sorted by model distance: nonbonded pdb=" O2B ATP A5301 " pdb="MG MG A5302 " model vdw 1.840 2.170 nonbonded pdb=" O CYS A3979 " pdb=" O LYS A3982 " model vdw 1.889 2.432 nonbonded pdb=" OE2 GLU A2098 " pdb="MG MG A5302 " model vdw 1.911 2.170 nonbonded pdb=" O GLY A1094 " pdb=" OG SER A1098 " model vdw 1.955 3.040 nonbonded pdb=" O ILE A5061 " pdb=" NZ LYS A5065 " model vdw 2.024 3.120 ... (remaining 300803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.006 0.334 36082 Z= 0.275 Angle : 0.550 20.097 48785 Z= 0.339 Chirality : 0.037 0.171 5535 Planarity : 0.003 0.039 6189 Dihedral : 14.811 89.816 13508 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 1.80 % Allowed : 13.38 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: -2.05 (0.12), residues: 4307 helix: -0.83 (0.09), residues: 2518 sheet: -2.11 (0.27), residues: 267 loop : -1.93 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1414 TYR 0.012 0.001 TYR A5018 PHE 0.020 0.001 PHE A 559 TRP 0.010 0.001 TRP A3183 HIS 0.005 0.001 HIS A4014 Details of bonding type rmsd covalent geometry : bond 0.00593 (36080) covalent geometry : angle 0.54975 (48785) hydrogen bonds : bond 0.13277 ( 1951) hydrogen bonds : angle 6.13958 ( 5673) metal coordination : bond 0.29981 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8109 (ttpp) REVERT: A 532 LEU cc_start: 0.8116 (mt) cc_final: 0.7916 (mt) REVERT: A 1042 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7096 (p0) REVERT: A 2593 TYR cc_start: 0.7703 (m-80) cc_final: 0.7444 (m-10) REVERT: A 4354 LYS cc_start: 0.9200 (tttp) cc_final: 0.8965 (ptmm) REVERT: A 4503 TYR cc_start: 0.7369 (m-80) cc_final: 0.6968 (m-80) outliers start: 71 outliers final: 29 residues processed: 281 average time/residue: 0.5444 time to fit residues: 189.9903 Evaluate side-chains 195 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1853 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3223 SER Chi-restraints excluded: chain A residue 3841 SER Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4142 SER Chi-restraints excluded: chain A residue 4280 VAL Chi-restraints excluded: chain A residue 4416 SER Chi-restraints excluded: chain A residue 4525 CYS Chi-restraints excluded: chain A residue 4733 SER Chi-restraints excluded: chain A residue 4881 THR Chi-restraints excluded: chain A residue 4922 SER Chi-restraints excluded: chain A residue 4965 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 780 HIS A1280 GLN A1376 ASN A1491 HIS A1784 GLN A2200 HIS A2787 GLN A3053 GLN A3303 HIS A3704 ASN A3995 GLN A4049 GLN A4051 HIS A4151 GLN A4617 GLN A4816 HIS A4905 ASN A4906 ASN A4919 HIS A5113 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.064722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.054394 restraints weight = 159932.630| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.62 r_work: 0.3281 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36082 Z= 0.142 Angle : 0.550 9.826 48785 Z= 0.283 Chirality : 0.040 0.215 5535 Planarity : 0.004 0.050 6189 Dihedral : 4.865 83.164 4784 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 13.79 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.14 (0.13), residues: 4307 helix: 0.86 (0.10), residues: 2561 sheet: -1.51 (0.27), residues: 276 loop : -0.80 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2358 TYR 0.016 0.001 TYR A1700 PHE 0.024 0.001 PHE A 559 TRP 0.018 0.001 TRP A 643 HIS 0.018 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00319 (36080) covalent geometry : angle 0.55047 (48785) hydrogen bonds : bond 0.04074 ( 1951) hydrogen bonds : angle 4.48249 ( 5673) metal coordination : bond 0.02745 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7689 (t80) cc_final: 0.7086 (OUTLIER) REVERT: A 432 LEU cc_start: 0.8692 (tt) cc_final: 0.8399 (tm) REVERT: A 527 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8118 (pt0) REVERT: A 532 LEU cc_start: 0.8173 (mt) cc_final: 0.7941 (mt) REVERT: A 561 PHE cc_start: 0.8265 (t80) cc_final: 0.8022 (OUTLIER) REVERT: A 588 ARG cc_start: 0.7688 (tpm170) cc_final: 0.7403 (tpm170) REVERT: A 742 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 1029 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 1303 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6321 (mt) REVERT: A 1489 MET cc_start: 0.9006 (mmt) cc_final: 0.8597 (mpt) REVERT: A 1761 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: A 2358 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8166 (mpp-170) REVERT: A 2593 TYR cc_start: 0.8235 (m-80) cc_final: 0.7879 (m-10) REVERT: A 2721 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 3436 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 3450 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8333 (pp) REVERT: A 4098 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 4503 TYR cc_start: 0.7397 (m-80) cc_final: 0.6827 (m-80) REVERT: A 4558 VAL cc_start: 0.8894 (p) cc_final: 0.8649 (m) REVERT: A 5181 PHE cc_start: 0.7658 (t80) cc_final: 0.7379 (t80) outliers start: 65 outliers final: 20 residues processed: 242 average time/residue: 0.5493 time to fit residues: 165.5704 Evaluate side-chains 192 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1761 MET Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 131 optimal weight: 2.9990 chunk 369 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 273 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 433 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 75 optimal weight: 0.0670 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1291 GLN A1342 GLN A1491 HIS A3167 ASN A3303 HIS A3819 GLN ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4275 HIS A4617 GLN A4892 ASN A4919 HIS A5122 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.062941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052404 restraints weight = 161708.377| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.73 r_work: 0.3185 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36082 Z= 0.194 Angle : 0.543 8.177 48785 Z= 0.278 Chirality : 0.041 0.218 5535 Planarity : 0.004 0.118 6189 Dihedral : 4.601 77.168 4751 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 2.03 % Allowed : 14.37 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.85 (0.13), residues: 4307 helix: 1.39 (0.10), residues: 2571 sheet: -1.12 (0.28), residues: 278 loop : -0.49 (0.18), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3914 TYR 0.014 0.001 TYR A1700 PHE 0.020 0.001 PHE A 559 TRP 0.016 0.001 TRP A 643 HIS 0.016 0.001 HIS A4919 Details of bonding type rmsd covalent geometry : bond 0.00457 (36080) covalent geometry : angle 0.54280 (48785) hydrogen bonds : bond 0.04055 ( 1951) hydrogen bonds : angle 4.26946 ( 5673) metal coordination : bond 0.00433 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 186 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7629 (t80) cc_final: 0.6909 (t80) REVERT: A 432 LEU cc_start: 0.8766 (tt) cc_final: 0.8475 (tm) REVERT: A 527 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8227 (pt0) REVERT: A 532 LEU cc_start: 0.8259 (mt) cc_final: 0.7991 (mt) REVERT: A 561 PHE cc_start: 0.8227 (t80) cc_final: 0.8008 (t80) REVERT: A 588 ARG cc_start: 0.7785 (tpm170) cc_final: 0.6761 (tpm170) REVERT: A 742 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 1029 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 1396 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5509 (tp) REVERT: A 1489 MET cc_start: 0.8957 (mmt) cc_final: 0.8748 (mmt) REVERT: A 2593 TYR cc_start: 0.8236 (m-80) cc_final: 0.7845 (m-10) REVERT: A 2721 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 3450 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 3546 MET cc_start: 0.8408 (mtp) cc_final: 0.8204 (mtm) REVERT: A 3891 MET cc_start: 0.8394 (mtp) cc_final: 0.8175 (mtt) REVERT: A 4098 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 4402 LYS cc_start: 0.9048 (tppt) cc_final: 0.8780 (tppp) REVERT: A 4503 TYR cc_start: 0.7509 (m-80) cc_final: 0.6955 (m-80) REVERT: A 4558 VAL cc_start: 0.8961 (p) cc_final: 0.8708 (m) REVERT: A 4919 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (m90) REVERT: A 5108 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7833 (t70) outliers start: 80 outliers final: 27 residues processed: 251 average time/residue: 0.5458 time to fit residues: 168.9249 Evaluate side-chains 205 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4817 SER Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 5108 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 302 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 chunk 418 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 370 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1376 ASN A1491 HIS A3303 HIS ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 HIS A4617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.062720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052178 restraints weight = 161426.822| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.75 r_work: 0.3176 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36082 Z= 0.168 Angle : 0.521 9.120 48785 Z= 0.266 Chirality : 0.040 0.151 5535 Planarity : 0.004 0.052 6189 Dihedral : 4.538 73.924 4751 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 14.80 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.17 (0.13), residues: 4307 helix: 1.62 (0.10), residues: 2569 sheet: -0.91 (0.28), residues: 278 loop : -0.32 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1823 TYR 0.014 0.001 TYR A1700 PHE 0.028 0.001 PHE A 559 TRP 0.017 0.001 TRP A 591 HIS 0.012 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00393 (36080) covalent geometry : angle 0.52082 (48785) hydrogen bonds : bond 0.03785 ( 1951) hydrogen bonds : angle 4.15126 ( 5673) metal coordination : bond 0.00285 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7688 (t80) cc_final: 0.6872 (t80) REVERT: A 432 LEU cc_start: 0.8743 (tt) cc_final: 0.8473 (tm) REVERT: A 527 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8226 (pt0) REVERT: A 532 LEU cc_start: 0.8249 (mt) cc_final: 0.7949 (mt) REVERT: A 561 PHE cc_start: 0.8238 (t80) cc_final: 0.8012 (t80) REVERT: A 588 ARG cc_start: 0.7735 (tpm170) cc_final: 0.7214 (tpm170) REVERT: A 742 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 823 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7582 (tpp) REVERT: A 1010 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8737 (mp10) REVERT: A 1022 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 1029 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 1069 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8756 (mtmm) REVERT: A 1398 GLN cc_start: 0.7736 (tp40) cc_final: 0.7372 (tp-100) REVERT: A 2593 TYR cc_start: 0.8236 (m-80) cc_final: 0.7848 (m-10) REVERT: A 2721 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 3450 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8357 (pp) REVERT: A 3891 MET cc_start: 0.8440 (mtp) cc_final: 0.8220 (mtt) REVERT: A 3944 LEU cc_start: 0.8858 (mm) cc_final: 0.8629 (mp) REVERT: A 4098 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8164 (m) REVERT: A 4402 LYS cc_start: 0.9050 (tppt) cc_final: 0.8804 (tppp) REVERT: A 4503 TYR cc_start: 0.7524 (m-80) cc_final: 0.6984 (m-80) REVERT: A 5108 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7824 (t70) REVERT: A 5181 PHE cc_start: 0.7718 (t80) cc_final: 0.7380 (t80) outliers start: 78 outliers final: 36 residues processed: 254 average time/residue: 0.5194 time to fit residues: 163.9582 Evaluate side-chains 216 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4918 LEU Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5108 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 320 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 110 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A1491 HIS A2178 GLN A3065 GLN A3303 HIS ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 HIS A4617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.063036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052608 restraints weight = 162011.085| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.68 r_work: 0.3191 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36082 Z= 0.117 Angle : 0.492 9.857 48785 Z= 0.250 Chirality : 0.039 0.271 5535 Planarity : 0.004 0.053 6189 Dihedral : 4.421 71.465 4751 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 1.95 % Allowed : 15.49 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.47 (0.13), residues: 4307 helix: 1.85 (0.10), residues: 2570 sheet: -0.81 (0.29), residues: 274 loop : -0.18 (0.18), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1823 TYR 0.014 0.001 TYR A1275 PHE 0.027 0.001 PHE A 559 TRP 0.020 0.001 TRP A 591 HIS 0.012 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00268 (36080) covalent geometry : angle 0.49160 (48785) hydrogen bonds : bond 0.03481 ( 1951) hydrogen bonds : angle 4.02923 ( 5673) metal coordination : bond 0.00225 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 181 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7701 (t80) cc_final: 0.7024 (t80) REVERT: A 432 LEU cc_start: 0.8706 (tt) cc_final: 0.8506 (tm) REVERT: A 532 LEU cc_start: 0.8294 (mt) cc_final: 0.7981 (mt) REVERT: A 561 PHE cc_start: 0.8244 (t80) cc_final: 0.8028 (t80) REVERT: A 588 ARG cc_start: 0.7698 (tpm170) cc_final: 0.7263 (tpm170) REVERT: A 742 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 823 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7512 (tpp) REVERT: A 1029 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 1302 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: A 1398 GLN cc_start: 0.7697 (tp40) cc_final: 0.7212 (tp-100) REVERT: A 2593 TYR cc_start: 0.8239 (m-80) cc_final: 0.7928 (m-10) REVERT: A 2721 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 3450 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8407 (pp) REVERT: A 3935 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 4098 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8276 (m) REVERT: A 4402 LYS cc_start: 0.9115 (tppt) cc_final: 0.8836 (tppp) REVERT: A 4404 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9014 (tp) REVERT: A 4415 ILE cc_start: 0.8763 (mt) cc_final: 0.8190 (tt) REVERT: A 4503 TYR cc_start: 0.7719 (m-80) cc_final: 0.7251 (m-80) REVERT: A 4558 VAL cc_start: 0.9017 (p) cc_final: 0.8759 (m) REVERT: A 5181 PHE cc_start: 0.7821 (t80) cc_final: 0.7538 (t80) outliers start: 77 outliers final: 38 residues processed: 249 average time/residue: 0.5221 time to fit residues: 161.2575 Evaluate side-chains 217 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3954 LEU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4404 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain A residue 5103 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 359 optimal weight: 5.9990 chunk 427 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 339 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 307 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A1491 HIS A2357 GLN A3303 HIS A3951 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.062965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052163 restraints weight = 161377.986| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.93 r_work: 0.3173 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36082 Z= 0.120 Angle : 0.497 11.224 48785 Z= 0.250 Chirality : 0.038 0.227 5535 Planarity : 0.004 0.051 6189 Dihedral : 4.374 70.221 4751 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.88 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 15.79 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.64 (0.13), residues: 4307 helix: 1.98 (0.10), residues: 2565 sheet: -0.71 (0.30), residues: 272 loop : -0.09 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1823 TYR 0.014 0.001 TYR A1275 PHE 0.026 0.001 PHE A 559 TRP 0.019 0.001 TRP A 591 HIS 0.013 0.001 HIS A1491 Details of bonding type rmsd covalent geometry : bond 0.00278 (36080) covalent geometry : angle 0.49712 (48785) hydrogen bonds : bond 0.03448 ( 1951) hydrogen bonds : angle 3.98011 ( 5673) metal coordination : bond 0.00273 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7708 (t80) cc_final: 0.7017 (t80) REVERT: A 432 LEU cc_start: 0.8738 (tt) cc_final: 0.8518 (tm) REVERT: A 532 LEU cc_start: 0.8251 (mt) cc_final: 0.7943 (mt) REVERT: A 561 PHE cc_start: 0.8222 (t80) cc_final: 0.8017 (t80) REVERT: A 588 ARG cc_start: 0.7771 (tpm170) cc_final: 0.7298 (tpm170) REVERT: A 742 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 823 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7575 (tpp) REVERT: A 1029 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 1302 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 1398 GLN cc_start: 0.7732 (tp40) cc_final: 0.7225 (tp-100) REVERT: A 1457 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 1758 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8467 (mmm160) REVERT: A 2593 TYR cc_start: 0.8250 (m-80) cc_final: 0.7868 (m-10) REVERT: A 2626 MET cc_start: 0.9025 (mmm) cc_final: 0.8762 (mpp) REVERT: A 2721 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 3450 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (pp) REVERT: A 3891 MET cc_start: 0.8454 (mtp) cc_final: 0.8226 (mtt) REVERT: A 3935 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 4098 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8120 (m) REVERT: A 4402 LYS cc_start: 0.9069 (tppt) cc_final: 0.8805 (tppp) REVERT: A 4415 ILE cc_start: 0.8741 (mt) cc_final: 0.8161 (tt) REVERT: A 4471 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 4503 TYR cc_start: 0.7585 (m-80) cc_final: 0.7060 (m-80) REVERT: A 4558 VAL cc_start: 0.8950 (p) cc_final: 0.8651 (m) REVERT: A 5108 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7877 (t70) REVERT: A 5181 PHE cc_start: 0.7766 (t80) cc_final: 0.7386 (t80) outliers start: 76 outliers final: 40 residues processed: 242 average time/residue: 0.5255 time to fit residues: 157.5502 Evaluate side-chains 219 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3345 THR Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4471 SER Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5108 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 239 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1491 HIS A3303 HIS A3951 HIS A3995 GLN A4051 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.062185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051263 restraints weight = 162161.945| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.93 r_work: 0.3107 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 36082 Z= 0.200 Angle : 0.546 13.127 48785 Z= 0.274 Chirality : 0.040 0.241 5535 Planarity : 0.004 0.051 6189 Dihedral : 4.531 67.397 4751 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.08 % Allowed : 15.89 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.56 (0.13), residues: 4307 helix: 1.91 (0.10), residues: 2572 sheet: -0.69 (0.29), residues: 282 loop : -0.10 (0.18), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3914 TYR 0.015 0.001 TYR A3356 PHE 0.028 0.001 PHE A 559 TRP 0.018 0.001 TRP A 591 HIS 0.010 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00473 (36080) covalent geometry : angle 0.54596 (48785) hydrogen bonds : bond 0.03807 ( 1951) hydrogen bonds : angle 4.04519 ( 5673) metal coordination : bond 0.00425 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 178 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7743 (t80) cc_final: 0.7136 (t80) REVERT: A 432 LEU cc_start: 0.8753 (tt) cc_final: 0.8490 (tm) REVERT: A 532 LEU cc_start: 0.8341 (mt) cc_final: 0.8018 (mt) REVERT: A 561 PHE cc_start: 0.8224 (t80) cc_final: 0.8003 (t80) REVERT: A 588 ARG cc_start: 0.7842 (tpm170) cc_final: 0.7368 (tpm170) REVERT: A 742 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 823 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7636 (tpp) REVERT: A 1302 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: A 1398 GLN cc_start: 0.7785 (tp40) cc_final: 0.7279 (tp-100) REVERT: A 1757 MET cc_start: 0.7867 (ttt) cc_final: 0.7651 (ttm) REVERT: A 1758 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8399 (mmm160) REVERT: A 3450 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8424 (pp) REVERT: A 3935 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 4098 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 4402 LYS cc_start: 0.9022 (tppt) cc_final: 0.8791 (tppp) REVERT: A 4415 ILE cc_start: 0.8778 (mt) cc_final: 0.8364 (tt) REVERT: A 4471 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 4503 TYR cc_start: 0.7736 (m-80) cc_final: 0.7250 (m-80) REVERT: A 5108 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7851 (t70) REVERT: A 5181 PHE cc_start: 0.7760 (t80) cc_final: 0.7355 (t80) outliers start: 82 outliers final: 46 residues processed: 250 average time/residue: 0.5100 time to fit residues: 159.2822 Evaluate side-chains 224 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1319 SER Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3345 THR Chi-restraints excluded: chain A residue 3423 VAL Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3944 LEU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4471 SER Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 268 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 429 optimal weight: 0.4980 chunk 120 optimal weight: 7.9990 chunk 154 optimal weight: 0.1980 chunk 90 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 110 optimal weight: 0.0770 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1491 HIS A3303 HIS A3951 HIS A3995 GLN A4051 HIS ** A4617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5059 GLN A5113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.062993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.052243 restraints weight = 161598.639| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.67 r_work: 0.3192 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 36082 Z= 0.100 Angle : 0.505 14.430 48785 Z= 0.253 Chirality : 0.038 0.250 5535 Planarity : 0.004 0.051 6189 Dihedral : 4.406 65.314 4751 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.67 % Allowed : 16.40 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.81 (0.13), residues: 4307 helix: 2.11 (0.10), residues: 2558 sheet: -0.60 (0.29), residues: 282 loop : 0.02 (0.18), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1823 TYR 0.013 0.001 TYR A1314 PHE 0.028 0.001 PHE A 559 TRP 0.019 0.001 TRP A 591 HIS 0.018 0.001 HIS A1491 Details of bonding type rmsd covalent geometry : bond 0.00217 (36080) covalent geometry : angle 0.50526 (48785) hydrogen bonds : bond 0.03343 ( 1951) hydrogen bonds : angle 3.93373 ( 5673) metal coordination : bond 0.00273 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7677 (t80) cc_final: 0.7158 (t80) REVERT: A 524 LYS cc_start: 0.8409 (mptt) cc_final: 0.7964 (mppt) REVERT: A 532 LEU cc_start: 0.8290 (mt) cc_final: 0.7942 (mt) REVERT: A 588 ARG cc_start: 0.7836 (tpm170) cc_final: 0.7090 (tpm170) REVERT: A 742 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 1302 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: A 1398 GLN cc_start: 0.7712 (tp40) cc_final: 0.7124 (tp-100) REVERT: A 2626 MET cc_start: 0.8907 (mmm) cc_final: 0.8666 (mmm) REVERT: A 3450 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8410 (pp) REVERT: A 3891 MET cc_start: 0.8412 (mtp) cc_final: 0.8183 (mtt) REVERT: A 3901 HIS cc_start: 0.7851 (t-170) cc_final: 0.7519 (t-90) REVERT: A 3935 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 3972 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 4064 MET cc_start: 0.7883 (mmm) cc_final: 0.7578 (tpp) REVERT: A 4098 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 4398 GLU cc_start: 0.8604 (pp20) cc_final: 0.8318 (pp20) REVERT: A 4402 LYS cc_start: 0.9014 (tppt) cc_final: 0.8779 (tppp) REVERT: A 4415 ILE cc_start: 0.8806 (mt) cc_final: 0.8311 (tt) REVERT: A 4503 TYR cc_start: 0.7645 (m-80) cc_final: 0.7160 (m-80) REVERT: A 5181 PHE cc_start: 0.7718 (t80) cc_final: 0.7321 (t80) outliers start: 66 outliers final: 41 residues processed: 233 average time/residue: 0.5584 time to fit residues: 164.4394 Evaluate side-chains 214 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3345 THR Chi-restraints excluded: chain A residue 3423 VAL Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3954 LEU Chi-restraints excluded: chain A residue 3972 GLU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4098 VAL Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 200 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 309 optimal weight: 0.7980 chunk 278 optimal weight: 0.1980 chunk 269 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 307 optimal weight: 0.9990 chunk 419 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1491 HIS A2225 GLN A3303 HIS A3951 HIS A4051 HIS ** A4617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.062959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.052246 restraints weight = 161833.947| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.82 r_work: 0.3181 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 36082 Z= 0.106 Angle : 0.509 14.527 48785 Z= 0.254 Chirality : 0.038 0.178 5535 Planarity : 0.004 0.076 6189 Dihedral : 4.329 65.252 4751 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 1.60 % Allowed : 16.58 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.95 (0.13), residues: 4307 helix: 2.20 (0.10), residues: 2553 sheet: -0.50 (0.30), residues: 282 loop : 0.10 (0.18), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1758 TYR 0.017 0.001 TYR A1314 PHE 0.035 0.001 PHE A 561 TRP 0.019 0.001 TRP A 591 HIS 0.010 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00239 (36080) covalent geometry : angle 0.50879 (48785) hydrogen bonds : bond 0.03311 ( 1951) hydrogen bonds : angle 3.89225 ( 5673) metal coordination : bond 0.00299 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 176 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7650 (t80) cc_final: 0.7122 (t80) REVERT: A 524 LYS cc_start: 0.8424 (mptt) cc_final: 0.7991 (mppt) REVERT: A 532 LEU cc_start: 0.8229 (mt) cc_final: 0.7915 (mt) REVERT: A 742 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 823 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: A 1398 GLN cc_start: 0.7697 (tp40) cc_final: 0.7169 (tp-100) REVERT: A 2626 MET cc_start: 0.8915 (mmm) cc_final: 0.8608 (mmm) REVERT: A 2855 MET cc_start: 0.8441 (mmt) cc_final: 0.8232 (mmp) REVERT: A 3450 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 3891 MET cc_start: 0.8435 (mtp) cc_final: 0.8217 (mtm) REVERT: A 3901 HIS cc_start: 0.7938 (t-170) cc_final: 0.7615 (t-90) REVERT: A 3935 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (mm) REVERT: A 3972 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 4064 MET cc_start: 0.7874 (mmm) cc_final: 0.7607 (tpp) REVERT: A 4252 MET cc_start: 0.8036 (mmt) cc_final: 0.7771 (mmt) REVERT: A 4398 GLU cc_start: 0.8625 (pp20) cc_final: 0.8336 (pp20) REVERT: A 4402 LYS cc_start: 0.8974 (tppt) cc_final: 0.8729 (tppp) REVERT: A 4415 ILE cc_start: 0.8777 (mt) cc_final: 0.8229 (tt) REVERT: A 4503 TYR cc_start: 0.7637 (m-80) cc_final: 0.7150 (m-80) REVERT: A 5181 PHE cc_start: 0.7663 (t80) cc_final: 0.7265 (t80) outliers start: 63 outliers final: 40 residues processed: 230 average time/residue: 0.5343 time to fit residues: 152.1655 Evaluate side-chains 215 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2337 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3201 VAL Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3345 THR Chi-restraints excluded: chain A residue 3423 VAL Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3972 GLU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 313 optimal weight: 0.7980 chunk 228 optimal weight: 0.0370 chunk 167 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 358 optimal weight: 0.0040 chunk 18 optimal weight: 5.9990 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1491 HIS A3303 HIS A3951 HIS A3995 GLN A4051 HIS ** A4617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.052368 restraints weight = 162335.568| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.82 r_work: 0.3251 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 36082 Z= 0.108 Angle : 0.524 14.639 48785 Z= 0.258 Chirality : 0.038 0.198 5535 Planarity : 0.004 0.092 6189 Dihedral : 4.290 72.982 4751 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 1.39 % Allowed : 16.81 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.98 (0.13), residues: 4307 helix: 2.21 (0.10), residues: 2561 sheet: -0.40 (0.30), residues: 282 loop : 0.12 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1823 TYR 0.015 0.001 TYR A1314 PHE 0.032 0.001 PHE A1381 TRP 0.019 0.001 TRP A 591 HIS 0.010 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00245 (36080) covalent geometry : angle 0.52364 (48785) hydrogen bonds : bond 0.03271 ( 1951) hydrogen bonds : angle 3.89031 ( 5673) metal coordination : bond 0.00313 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8614 Ramachandran restraints generated. 4307 Oldfield, 0 Emsley, 4307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.7680 (t80) cc_final: 0.7228 (t80) REVERT: A 524 LYS cc_start: 0.8365 (mptt) cc_final: 0.7968 (mppt) REVERT: A 532 LEU cc_start: 0.8338 (mt) cc_final: 0.8039 (mt) REVERT: A 742 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 823 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7429 (tpp) REVERT: A 1398 GLN cc_start: 0.7473 (tp40) cc_final: 0.7084 (tp-100) REVERT: A 3450 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8523 (pp) REVERT: A 3856 MET cc_start: 0.7867 (ttt) cc_final: 0.7482 (ttp) REVERT: A 3891 MET cc_start: 0.8578 (mtp) cc_final: 0.8336 (mtt) REVERT: A 3901 HIS cc_start: 0.7898 (t-170) cc_final: 0.7584 (t-90) REVERT: A 3972 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: A 4252 MET cc_start: 0.7949 (mmt) cc_final: 0.7613 (mmt) REVERT: A 4398 GLU cc_start: 0.8585 (pp20) cc_final: 0.8319 (pp20) REVERT: A 4402 LYS cc_start: 0.9022 (tppt) cc_final: 0.8768 (tppp) REVERT: A 4415 ILE cc_start: 0.8715 (mt) cc_final: 0.8160 (tt) REVERT: A 4503 TYR cc_start: 0.7670 (m-80) cc_final: 0.7193 (m-80) REVERT: A 4992 MET cc_start: 0.8599 (mmm) cc_final: 0.8269 (mmt) REVERT: A 5108 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7926 (t70) REVERT: A 5181 PHE cc_start: 0.7763 (t80) cc_final: 0.7388 (t80) outliers start: 55 outliers final: 39 residues processed: 222 average time/residue: 0.5855 time to fit residues: 159.3563 Evaluate side-chains 214 residues out of total 3945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 591 TRP Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 2050 VAL Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3345 THR Chi-restraints excluded: chain A residue 3423 VAL Chi-restraints excluded: chain A residue 3450 LEU Chi-restraints excluded: chain A residue 3452 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3954 LEU Chi-restraints excluded: chain A residue 3972 GLU Chi-restraints excluded: chain A residue 3984 THR Chi-restraints excluded: chain A residue 3986 SER Chi-restraints excluded: chain A residue 3990 SER Chi-restraints excluded: chain A residue 4052 ARG Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4353 ILE Chi-restraints excluded: chain A residue 4723 VAL Chi-restraints excluded: chain A residue 4788 LEU Chi-restraints excluded: chain A residue 4919 HIS Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 4971 LEU Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain A residue 5108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 129 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 384 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1491 HIS A2399 ASN A3303 HIS A3951 HIS A3995 GLN A4051 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.061746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.050789 restraints weight = 162529.643| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.93 r_work: 0.3328 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 36082 Z= 0.248 Angle : 0.605 17.319 48785 Z= 0.299 Chirality : 0.042 0.179 5535 Planarity : 0.004 0.125 6189 Dihedral : 4.482 71.525 4748 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 1.52 % Allowed : 16.70 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 1.70 (0.13), residues: 4307 helix: 1.99 (0.10), residues: 2552 sheet: -0.55 (0.30), residues: 282 loop : 0.02 (0.18), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A4417 TYR 0.016 0.001 TYR A3767 PHE 0.039 0.002 PHE A 561 TRP 0.019 0.002 TRP A1496 HIS 0.009 0.001 HIS A4989 Details of bonding type rmsd covalent geometry : bond 0.00588 (36080) covalent geometry : angle 0.60538 (48785) hydrogen bonds : bond 0.03993 ( 1951) hydrogen bonds : angle 4.07778 ( 5673) metal coordination : bond 0.00535 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9134.25 seconds wall clock time: 157 minutes 3.04 seconds (9423.04 seconds total)