Starting phenix.real_space_refine on Tue Oct 27 18:02:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.cif Found real_map, /net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27pz_81336/10_2026/27pz_81336.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 97 5.16 5 C 15689 2.51 5 N 4202 2.21 5 O 4645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24643 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3048, 24530 Classifications: {'peptide': 3048} Link IDs: {'PCIS': 2, 'PTRANS': 124, 'TRANS': 2921} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.52, per 1000 atoms: 0.18 Number of scatterers: 24643 At special positions: 0 Unit cell: (119.601, 151.902, 176.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 9 15.00 Mg 1 11.99 O 4645 8.00 N 4202 7.00 C 15689 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: 2.21 Conformation dependent library (CDL) restraints added in 901.0 milliseconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5810 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 21 sheets defined 62.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 1401 through 1407 removed outlier: 3.579A pdb=" N SER A1405 " --> pdb=" O TRP A1401 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1416 Processing helix chain 'A' and resid 1423 through 1437 Processing helix chain 'A' and resid 1442 through 1446 removed outlier: 3.627A pdb=" N ILE A1445 " --> pdb=" O PRO A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1473 removed outlier: 4.272A pdb=" N ALA A1466 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A1467 " --> pdb=" O LYS A1463 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A1473 " --> pdb=" O THR A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1486 removed outlier: 3.503A pdb=" N LYS A1486 " --> pdb=" O LYS A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1504 Processing helix chain 'A' and resid 1510 through 1541 removed outlier: 3.702A pdb=" N THR A1540 " --> pdb=" O GLU A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1576 removed outlier: 4.061A pdb=" N LYS A1564 " --> pdb=" O ASP A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1622 removed outlier: 3.824A pdb=" N ASP A1607 " --> pdb=" O ASP A1603 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A1622 " --> pdb=" O ILE A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1629 through 1652 removed outlier: 3.593A pdb=" N GLY A1652 " --> pdb=" O LYS A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.546A pdb=" N LEU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1661 " --> pdb=" O LEU A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1694 removed outlier: 3.965A pdb=" N PHE A1694 " --> pdb=" O GLN A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1700 Processing helix chain 'A' and resid 1701 through 1711 Processing helix chain 'A' and resid 1714 through 1718 Processing helix chain 'A' and resid 1721 through 1726 Processing helix chain 'A' and resid 1770 through 1793 Processing helix chain 'A' and resid 1799 through 1810 removed outlier: 3.682A pdb=" N TYR A1810 " --> pdb=" O TRP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1832 Processing helix chain 'A' and resid 1837 through 1864 removed outlier: 3.703A pdb=" N LEU A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1895 Processing helix chain 'A' and resid 1903 through 1908 Processing helix chain 'A' and resid 1920 through 1923 Processing helix chain 'A' and resid 1950 through 1966 Processing helix chain 'A' and resid 1979 through 1991 Processing helix chain 'A' and resid 2005 through 2020 removed outlier: 3.919A pdb=" N ARG A2011 " --> pdb=" O GLN A2007 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A2014 " --> pdb=" O SER A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2031 removed outlier: 3.577A pdb=" N ARG A2030 " --> pdb=" O GLU A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2052 removed outlier: 3.700A pdb=" N GLN A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A2052 " --> pdb=" O VAL A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2084 removed outlier: 4.189A pdb=" N GLY A2083 " --> pdb=" O GLY A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2116 Processing helix chain 'A' and resid 2120 through 2136 Proline residue: A2130 - end of helix removed outlier: 3.560A pdb=" N LYS A2133 " --> pdb=" O VAL A2129 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A2136 " --> pdb=" O PHE A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2166 removed outlier: 3.796A pdb=" N LYS A2165 " --> pdb=" O GLY A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2177 removed outlier: 3.655A pdb=" N THR A2175 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A2176 " --> pdb=" O PRO A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2203 removed outlier: 4.249A pdb=" N LYS A2182 " --> pdb=" O GLU A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 Processing helix chain 'A' and resid 2208 through 2210 No H-bonds generated for 'chain 'A' and resid 2208 through 2210' Processing helix chain 'A' and resid 2211 through 2217 removed outlier: 3.649A pdb=" N SER A2217 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2247 Processing helix chain 'A' and resid 2252 through 2269 removed outlier: 3.587A pdb=" N LYS A2258 " --> pdb=" O GLU A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2281 through 2298 Processing helix chain 'A' and resid 2312 through 2317 Processing helix chain 'A' and resid 2330 through 2338 Processing helix chain 'A' and resid 2404 through 2409 Processing helix chain 'A' and resid 2417 through 2421 removed outlier: 3.718A pdb=" N LEU A2421 " --> pdb=" O GLU A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2422 through 2437 Processing helix chain 'A' and resid 2440 through 2457 Processing helix chain 'A' and resid 2489 through 2503 removed outlier: 4.635A pdb=" N VAL A2494 " --> pdb=" O ALA A2490 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A2495 " --> pdb=" O GLY A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2522 removed outlier: 3.589A pdb=" N GLN A2521 " --> pdb=" O GLU A2517 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A2522 " --> pdb=" O ASP A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2529 through 2555 Processing helix chain 'A' and resid 2561 through 2582 removed outlier: 3.667A pdb=" N LEU A2574 " --> pdb=" O THR A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2585 No H-bonds generated for 'chain 'A' and resid 2583 through 2585' Processing helix chain 'A' and resid 2586 through 2600 removed outlier: 3.575A pdb=" N ASN A2592 " --> pdb=" O VAL A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2611 through 2613 No H-bonds generated for 'chain 'A' and resid 2611 through 2613' Processing helix chain 'A' and resid 2628 through 2630 No H-bonds generated for 'chain 'A' and resid 2628 through 2630' Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'A' and resid 2650 through 2666 removed outlier: 4.008A pdb=" N GLU A2666 " --> pdb=" O ALA A2662 " (cutoff:3.500A) Processing helix chain 'A' and resid 2679 through 2691 Processing helix chain 'A' and resid 2706 through 2717 removed outlier: 3.566A pdb=" N LEU A2710 " --> pdb=" O THR A2706 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A2713 " --> pdb=" O LEU A2709 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A2714 " --> pdb=" O LEU A2710 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2770 Processing helix chain 'A' and resid 2804 through 2809 Processing helix chain 'A' and resid 2820 through 2836 Processing helix chain 'A' and resid 2837 through 2843 Proline residue: A2840 - end of helix removed outlier: 3.505A pdb=" N ARG A2843 " --> pdb=" O PRO A2840 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2837 through 2843' Processing helix chain 'A' and resid 2845 through 2864 Processing helix chain 'A' and resid 2875 through 2892 removed outlier: 3.899A pdb=" N LEU A2879 " --> pdb=" O SER A2875 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A2892 " --> pdb=" O GLU A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2897 through 2914 Processing helix chain 'A' and resid 2919 through 2924 Processing helix chain 'A' and resid 2925 through 2938 Processing helix chain 'A' and resid 2964 through 2983 removed outlier: 4.260A pdb=" N GLU A2970 " --> pdb=" O SER A2966 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A2971 " --> pdb=" O ASP A2967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3006 Processing helix chain 'A' and resid 3023 through 3033 Processing helix chain 'A' and resid 3051 through 3059 Processing helix chain 'A' and resid 3082 through 3088 removed outlier: 3.542A pdb=" N ARG A3086 " --> pdb=" O SER A3082 " (cutoff:3.500A) Processing helix chain 'A' and resid 3089 through 3092 removed outlier: 3.974A pdb=" N ALA A3092 " --> pdb=" O THR A3089 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3089 through 3092' Processing helix chain 'A' and resid 3104 through 3113 Processing helix chain 'A' and resid 3115 through 3119 removed outlier: 3.593A pdb=" N ARG A3118 " --> pdb=" O THR A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3128 through 3138 removed outlier: 4.161A pdb=" N TYR A3132 " --> pdb=" O GLU A3128 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A3135 " --> pdb=" O LYS A3131 " (cutoff:3.500A) Processing helix chain 'A' and resid 3160 through 3168 removed outlier: 4.566A pdb=" N ASN A3166 " --> pdb=" O PRO A3162 " (cutoff:3.500A) Processing helix chain 'A' and resid 3177 through 3189 Processing helix chain 'A' and resid 3202 through 3213 Processing helix chain 'A' and resid 3222 through 3250 removed outlier: 3.594A pdb=" N GLY A3239 " --> pdb=" O HIS A3235 " (cutoff:3.500A) Processing helix chain 'A' and resid 3256 through 3310 Processing helix chain 'A' and resid 3553 through 3587 removed outlier: 3.561A pdb=" N GLY A3572 " --> pdb=" O ASN A3568 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A3573 " --> pdb=" O SER A3569 " (cutoff:3.500A) Processing helix chain 'A' and resid 3587 through 3602 Processing helix chain 'A' and resid 3603 through 3605 No H-bonds generated for 'chain 'A' and resid 3603 through 3605' Processing helix chain 'A' and resid 3606 through 3625 Processing helix chain 'A' and resid 3633 through 3638 Processing helix chain 'A' and resid 3640 through 3650 removed outlier: 3.856A pdb=" N ASN A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A3647 " --> pdb=" O GLU A3643 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A3648 " --> pdb=" O ARG A3644 " (cutoff:3.500A) Processing helix chain 'A' and resid 3655 through 3667 Processing helix chain 'A' and resid 3679 through 3689 removed outlier: 3.546A pdb=" N GLU A3683 " --> pdb=" O GLY A3679 " (cutoff:3.500A) Processing helix chain 'A' and resid 3690 through 3693 Processing helix chain 'A' and resid 3703 through 3715 Processing helix chain 'A' and resid 3722 through 3726 removed outlier: 4.042A pdb=" N ASN A3725 " --> pdb=" O ASP A3722 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A3726 " --> pdb=" O VAL A3723 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3722 through 3726' Processing helix chain 'A' and resid 3727 through 3729 No H-bonds generated for 'chain 'A' and resid 3727 through 3729' Processing helix chain 'A' and resid 3730 through 3735 Processing helix chain 'A' and resid 3774 through 3779 Processing helix chain 'A' and resid 3789 through 3806 Processing helix chain 'A' and resid 3806 through 3815 Processing helix chain 'A' and resid 3816 through 3841 removed outlier: 3.887A pdb=" N GLN A3824 " --> pdb=" O GLN A3820 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A3825 " --> pdb=" O GLY A3821 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A3841 " --> pdb=" O ALA A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.531A pdb=" N LEU A3846 " --> pdb=" O GLY A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3849 through 3903 removed outlier: 3.750A pdb=" N SER A3853 " --> pdb=" O ASP A3849 " (cutoff:3.500A) Proline residue: A3888 - end of helix Processing helix chain 'A' and resid 3904 through 3906 No H-bonds generated for 'chain 'A' and resid 3904 through 3906' Processing helix chain 'A' and resid 3912 through 3925 removed outlier: 3.524A pdb=" N PHE A3916 " --> pdb=" O SER A3912 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3931 removed outlier: 3.703A pdb=" N VAL A3931 " --> pdb=" O PRO A3928 " (cutoff:3.500A) Processing helix chain 'A' and resid 3935 through 3956 removed outlier: 3.785A pdb=" N VAL A3941 " --> pdb=" O ASN A3937 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A3945 " --> pdb=" O VAL A3941 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE A3948 " --> pdb=" O SER A3944 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A3949 " --> pdb=" O LYS A3945 " (cutoff:3.500A) Processing helix chain 'A' and resid 3960 through 3964 Processing helix chain 'A' and resid 3965 through 3976 Processing helix chain 'A' and resid 3984 through 3993 Processing helix chain 'A' and resid 3997 through 4001 Processing helix chain 'A' and resid 4005 through 4009 Processing helix chain 'A' and resid 4015 through 4027 removed outlier: 3.525A pdb=" N TRP A4019 " --> pdb=" O THR A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4028 through 4031 Processing helix chain 'A' and resid 4032 through 4040 Processing helix chain 'A' and resid 4059 through 4070 Processing helix chain 'A' and resid 4074 through 4089 removed outlier: 3.614A pdb=" N SER A4078 " --> pdb=" O SER A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4090 through 4092 No H-bonds generated for 'chain 'A' and resid 4090 through 4092' Processing helix chain 'A' and resid 4093 through 4106 Processing helix chain 'A' and resid 4117 through 4124 Processing helix chain 'A' and resid 4143 through 4153 removed outlier: 4.832A pdb=" N LEU A4149 " --> pdb=" O LYS A4145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A4151 " --> pdb=" O ASP A4147 " (cutoff:3.500A) Processing helix chain 'A' and resid 4164 through 4182 removed outlier: 4.070A pdb=" N GLU A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A4180 " --> pdb=" O TYR A4176 " (cutoff:3.500A) Processing helix chain 'A' and resid 4189 through 4192 Processing helix chain 'A' and resid 4193 through 4205 removed outlier: 3.886A pdb=" N VAL A4198 " --> pdb=" O PRO A4194 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN A4199 " --> pdb=" O GLN A4195 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A4202 " --> pdb=" O VAL A4198 " (cutoff:3.500A) Processing helix chain 'A' and resid 4226 through 4233 Processing helix chain 'A' and resid 4243 through 4254 removed outlier: 3.866A pdb=" N GLY A4254 " --> pdb=" O HIS A4250 " (cutoff:3.500A) Processing helix chain 'A' and resid 4256 through 4261 Processing helix chain 'A' and resid 4264 through 4282 removed outlier: 4.341A pdb=" N SER A4268 " --> pdb=" O PRO A4264 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG A4269 " --> pdb=" O ALA A4265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A4282 " --> pdb=" O HIS A4278 " (cutoff:3.500A) Processing helix chain 'A' and resid 4283 through 4288 removed outlier: 3.790A pdb=" N ILE A4288 " --> pdb=" O LEU A4285 " (cutoff:3.500A) Processing helix chain 'A' and resid 4299 through 4319 removed outlier: 3.762A pdb=" N LEU A4303 " --> pdb=" O ASN A4299 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A4317 " --> pdb=" O TRP A4313 " (cutoff:3.500A) Processing helix chain 'A' and resid 4330 through 4341 Processing helix chain 'A' and resid 4349 through 4364 removed outlier: 3.812A pdb=" N LEU A4355 " --> pdb=" O PHE A4351 " (cutoff:3.500A) Processing helix chain 'A' and resid 4365 through 4370 Processing helix chain 'A' and resid 4377 through 4380 Processing helix chain 'A' and resid 4388 through 4398 removed outlier: 3.543A pdb=" N PHE A4392 " --> pdb=" O THR A4388 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A4398 " --> pdb=" O LYS A4394 " (cutoff:3.500A) Processing helix chain 'A' and resid 4404 through 4409 removed outlier: 3.658A pdb=" N GLY A4409 " --> pdb=" O ILE A4406 " (cutoff:3.500A) Processing helix chain 'A' and resid 4413 through 4443 removed outlier: 4.227A pdb=" N ASP A4443 " --> pdb=" O ASP A4439 " (cutoff:3.500A) Processing helix chain 'A' and resid 4459 through 4477 removed outlier: 3.643A pdb=" N ALA A4464 " --> pdb=" O ASP A4460 " (cutoff:3.500A) Processing helix chain 'A' and resid 4488 through 4492 removed outlier: 3.998A pdb=" N LYS A4492 " --> pdb=" O GLN A4489 " (cutoff:3.500A) Processing helix chain 'A' and resid 4493 through 4526 Processing helix chain 'A' and resid 4533 through 4538 removed outlier: 3.694A pdb=" N LEU A4537 " --> pdb=" O TYR A4533 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A4538 " --> pdb=" O LEU A4534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4533 through 4538' Processing helix chain 'A' and resid 4539 through 4544 removed outlier: 3.787A pdb=" N GLY A4544 " --> pdb=" O ILE A4541 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4581 Processing helix chain 'A' and resid 4592 through 4594 No H-bonds generated for 'chain 'A' and resid 4592 through 4594' Processing helix chain 'A' and resid 4596 through 4612 removed outlier: 3.841A pdb=" N TYR A4600 " --> pdb=" O ASN A4596 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A4612 " --> pdb=" O ALA A4608 " (cutoff:3.500A) Processing helix chain 'A' and resid 4676 through 4685 removed outlier: 3.817A pdb=" N ASN A4681 " --> pdb=" O ILE A4678 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER A4683 " --> pdb=" O ASN A4680 " (cutoff:3.500A) Processing helix chain 'A' and resid 4712 through 4720 removed outlier: 3.796A pdb=" N SER A4720 " --> pdb=" O TRP A4716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1545 through 1548 removed outlier: 3.787A pdb=" N CYS A1552 " --> pdb=" O TYR A1548 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1729 through 1734 removed outlier: 7.605A pdb=" N GLY A1743 " --> pdb=" O LYS A1756 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N LYS A1756 " --> pdb=" O GLY A1743 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N SER A1745 " --> pdb=" O PHE A1754 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N PHE A1754 " --> pdb=" O SER A1745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1911 through 1914 Processing sheet with id=AA4, first strand: chain 'A' and resid 1969 through 1973 removed outlier: 6.547A pdb=" N GLY A1969 " --> pdb=" O ARG A2096 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET A2098 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN A1971 " --> pdb=" O MET A2098 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1995 through 1997 removed outlier: 6.473A pdb=" N LEU A1996 " --> pdb=" O CYS A2024 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY A2023 " --> pdb=" O PHE A2074 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 2056 through 2058 Processing sheet with id=AA7, first strand: chain 'A' and resid 2355 through 2356 removed outlier: 6.301A pdb=" N VAL A2272 " --> pdb=" O PHE A2395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2300 through 2303 removed outlier: 6.668A pdb=" N LYS A2300 " --> pdb=" O ARG A2350 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TRP A2352 " --> pdb=" O LYS A2300 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A2302 " --> pdb=" O TRP A2352 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG A2392 " --> pdb=" O LYS A2349 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS A2351 " --> pdb=" O ARG A2392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2319 through 2320 removed outlier: 3.700A pdb=" N SER A2319 " --> pdb=" O THR A2328 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A2328 " --> pdb=" O SER A2319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2376 through 2377 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2617 Processing sheet with id=AB3, first strand: chain 'A' and resid 2694 through 2699 removed outlier: 6.300A pdb=" N LEU A2672 " --> pdb=" O CYS A2792 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A2671 " --> pdb=" O LEU A2814 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2718 through 2722 removed outlier: 7.200A pdb=" N THR A2728 " --> pdb=" O LYS A2782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3036 through 3039 removed outlier: 6.310A pdb=" N SER A3036 " --> pdb=" O CYS A3070 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A3072 " --> pdb=" O SER A3036 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A3038 " --> pdb=" O ILE A3072 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A3069 " --> pdb=" O HIS A3142 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A3144 " --> pdb=" O ILE A3069 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE A3071 " --> pdb=" O VAL A3144 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A3146 " --> pdb=" O PHE A3071 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A3073 " --> pdb=" O THR A3146 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ALA A3012 " --> pdb=" O PHE A3145 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N MET A3147 " --> pdb=" O ALA A3012 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A3014 " --> pdb=" O MET A3147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3695 through 3698 removed outlier: 7.990A pdb=" N THR A3766 " --> pdb=" O PRO A3672 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A3674 " --> pdb=" O THR A3766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3739 through 3741 Processing sheet with id=AB8, first strand: chain 'A' and resid 4157 through 4161 removed outlier: 6.616A pdb=" N LYS A4158 " --> pdb=" O LEU A4186 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LYS A4188 " --> pdb=" O LYS A4158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A4160 " --> pdb=" O LYS A4188 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL A4185 " --> pdb=" O PHE A4216 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A4218 " --> pdb=" O VAL A4185 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A4187 " --> pdb=" O THR A4218 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU A4220 " --> pdb=" O LEU A4187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A4219 " --> pdb=" O LEU A4134 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A4133 " --> pdb=" O PHE A4236 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A4238 " --> pdb=" O LEU A4133 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A4135 " --> pdb=" O TYR A4238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4374 through 4376 Processing sheet with id=AC1, first strand: chain 'A' and resid 4589 through 4590 removed outlier: 6.848A pdb=" N THR A4668 " --> pdb=" O SER A4624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4661 through 4663 removed outlier: 3.769A pdb=" N PHE A4701 " --> pdb=" O VAL A4690 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4648 through 4650 1340 hydrogen bonds defined for protein. 3846 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: 7.09 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8046 1.34 - 1.46: 4050 1.46 - 1.57: 12900 1.57 - 1.69: 14 1.69 - 1.81: 163 Bond restraints: 25173 Sorted by residual: bond pdb=" C4 ADP A5001 " pdb=" C5 ADP A5001 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C4 ADP A5004 " pdb=" C5 ADP A5004 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP A5005 " pdb=" C5 ADP A5005 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C5 ADP A5005 " pdb=" C6 ADP A5005 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP A5001 " pdb=" C6 ADP A5001 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 25168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 33738 2.37 - 4.73: 336 4.73 - 7.10: 33 7.10 - 9.46: 16 9.46 - 11.83: 3 Bond angle restraints: 34126 Sorted by residual: angle pdb=" PB ATP A5002 " pdb=" O3B ATP A5002 " pdb=" PG ATP A5002 " ideal model delta sigma weight residual 139.87 128.04 11.83 1.00e+00 1.00e+00 1.40e+02 angle pdb=" PA ATP A5002 " pdb=" O3A ATP A5002 " pdb=" PB ATP A5002 " ideal model delta sigma weight residual 136.83 128.62 8.21 1.00e+00 1.00e+00 6.75e+01 angle pdb=" N GLU A2396 " pdb=" CA GLU A2396 " pdb=" CB GLU A2396 " ideal model delta sigma weight residual 110.71 119.20 -8.49 1.53e+00 4.27e-01 3.08e+01 angle pdb=" CA ASP A2356 " pdb=" CB ASP A2356 " pdb=" CG ASP A2356 " ideal model delta sigma weight residual 112.60 117.01 -4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N GLU A2287 " pdb=" CA GLU A2287 " pdb=" C GLU A2287 " ideal model delta sigma weight residual 112.90 107.72 5.18 1.31e+00 5.83e-01 1.56e+01 ... (remaining 34121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.01: 14661 27.01 - 54.03: 508 54.03 - 81.04: 65 81.04 - 108.05: 11 108.05 - 135.07: 4 Dihedral angle restraints: 15249 sinusoidal: 6319 harmonic: 8930 Sorted by residual: dihedral pdb=" C5' ADP A5004 " pdb=" O5' ADP A5004 " pdb=" PA ADP A5004 " pdb=" O2A ADP A5004 " ideal model delta sinusoidal sigma weight residual 300.00 164.94 135.07 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" O1B ADP A5004 " pdb=" O3A ADP A5004 " pdb=" PB ADP A5004 " pdb=" PA ADP A5004 " ideal model delta sinusoidal sigma weight residual 300.00 169.26 130.74 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O1B ADP A5001 " pdb=" O3A ADP A5001 " pdb=" PB ADP A5001 " pdb=" PA ADP A5001 " ideal model delta sinusoidal sigma weight residual 300.00 176.15 123.85 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 15246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2814 0.041 - 0.082: 782 0.082 - 0.123: 207 0.123 - 0.164: 26 0.164 - 0.205: 4 Chirality restraints: 3833 Sorted by residual: chirality pdb=" CA MET A2273 " pdb=" N MET A2273 " pdb=" C MET A2273 " pdb=" CB MET A2273 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE A3219 " pdb=" CA ILE A3219 " pdb=" CG1 ILE A3219 " pdb=" CG2 ILE A3219 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA VAL A2275 " pdb=" N VAL A2275 " pdb=" C VAL A2275 " pdb=" CB VAL A2275 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 3830 not shown) Planarity restraints: 4352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A2395 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C PHE A2395 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A2395 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A2396 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A2605 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A2606 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2606 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2606 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A4596 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A4597 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A4597 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A4597 " -0.026 5.00e-02 4.00e+02 ... (remaining 4349 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 2 1.85 - 2.61: 183 2.61 - 3.38: 33528 3.38 - 4.14: 58352 4.14 - 4.90: 111430 Nonbonded interactions: 203495 Sorted by model distance: nonbonded pdb=" OE2 GLU A2396 " pdb="MG MG A5003 " model vdw 1.091 2.170 nonbonded pdb=" OG1 THR A2283 " pdb="MG MG A5003 " model vdw 1.758 2.170 nonbonded pdb=" O ILE A4337 " pdb=" OG1 THR A4341 " model vdw 2.140 3.040 nonbonded pdb=" OG SER A2618 " pdb=" OD1 ASP A2621 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP A3655 " pdb=" OG SER A3792 " model vdw 2.143 3.040 ... (remaining 203490 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 25173 Z= 0.180 Angle : 0.596 11.827 34126 Z= 0.308 Chirality : 0.041 0.205 3833 Planarity : 0.004 0.049 4352 Dihedral : 13.777 135.068 9439 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3040 helix: 1.34 (0.13), residues: 1679 sheet: -1.64 (0.33), residues: 238 loop : 0.10 (0.20), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3559 TYR 0.019 0.001 TYR A3897 PHE 0.020 0.002 PHE A3073 TRP 0.023 0.001 TRP A2286 HIS 0.005 0.001 HIS A1877 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (25173) covalent geometry : angle 0.59611 / 0.31 (34126) hydrogen bonds : bond 0.13734 / 8.98 ( 1340) hydrogen bonds : angle 5.91692 / 4.11 ( 3846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7760 (mmt) cc_final: 0.7164 (mtm) REVERT: A 1593 ASP cc_start: 0.7346 (t0) cc_final: 0.6937 (m-30) REVERT: A 1671 ARG cc_start: 0.7219 (tmm160) cc_final: 0.6928 (ttt-90) REVERT: A 2504 GLN cc_start: 0.7209 (tt0) cc_final: 0.6982 (tm-30) REVERT: A 2505 TYR cc_start: 0.6536 (m-80) cc_final: 0.6011 (m-80) REVERT: A 2572 ARG cc_start: 0.7291 (tpt170) cc_final: 0.7060 (tpt-90) REVERT: A 2577 LEU cc_start: 0.7411 (tp) cc_final: 0.7209 (tp) REVERT: A 2591 GLU cc_start: 0.7254 (pt0) cc_final: 0.6920 (mt-10) REVERT: A 2648 ILE cc_start: 0.7779 (mm) cc_final: 0.7570 (mm) REVERT: A 3615 ARG cc_start: 0.7699 (tpm170) cc_final: 0.6642 (mtm-85) REVERT: A 3705 MET cc_start: 0.7524 (tpp) cc_final: 0.7232 (mmt) REVERT: A 3873 GLU cc_start: 0.6996 (tp30) cc_final: 0.6793 (tm-30) REVERT: A 4393 MET cc_start: 0.8045 (mmm) cc_final: 0.7845 (tpt) REVERT: A 4548 LYS cc_start: 0.8328 (mptt) cc_final: 0.7941 (mmtt) REVERT: A 4573 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 4625 SER cc_start: 0.8130 (t) cc_final: 0.7750 (p) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1900 time to fit residues: 106.7845 Evaluate side-chains 262 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A2229 GLN A2429 ASN A2565 GLN A2667 HIS A2700 ASN A3140 ASN A3731 ASN A3925 ASN A4038 GLN A4349 ASN A4434 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.230004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.183445 restraints weight = 25639.935| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.92 r_work: 0.3788 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25173 Z= 0.154 Angle : 0.566 8.824 34126 Z= 0.289 Chirality : 0.042 0.292 3833 Planarity : 0.004 0.049 4352 Dihedral : 7.640 125.892 3336 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.69 % Allowed : 5.21 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.16), residues: 3040 helix: 1.60 (0.13), residues: 1692 sheet: -1.69 (0.34), residues: 237 loop : 0.14 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3713 TYR 0.018 0.001 TYR A2828 PHE 0.027 0.002 PHE A2991 TRP 0.023 0.001 TRP A2286 HIS 0.005 0.001 HIS A1884 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (25173) covalent geometry : angle 0.56631 / 0.29 (34126) hydrogen bonds : bond 0.04254 / 2.74 ( 1340) hydrogen bonds : angle 4.56159 / 3.17 ( 3846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7663 (mmt) cc_final: 0.7073 (mtm) REVERT: A 1593 ASP cc_start: 0.7169 (t0) cc_final: 0.6658 (m-30) REVERT: A 2504 GLN cc_start: 0.7234 (tt0) cc_final: 0.6852 (tm-30) REVERT: A 2505 TYR cc_start: 0.6575 (m-80) cc_final: 0.5858 (m-80) REVERT: A 2591 GLU cc_start: 0.7400 (pt0) cc_final: 0.6983 (mt-10) REVERT: A 2630 LYS cc_start: 0.7201 (mttp) cc_final: 0.6955 (mttp) REVERT: A 2648 ILE cc_start: 0.7921 (mm) cc_final: 0.7717 (mm) REVERT: A 2752 ASP cc_start: 0.7228 (t0) cc_final: 0.6332 (m-30) REVERT: A 2753 LYS cc_start: 0.7955 (tptp) cc_final: 0.7705 (tptp) REVERT: A 3027 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7017 (mtt90) REVERT: A 3615 ARG cc_start: 0.7780 (tpm170) cc_final: 0.6608 (mtm-85) REVERT: A 3713 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7928 (mtp85) REVERT: A 3800 GLU cc_start: 0.8213 (tp30) cc_final: 0.7593 (tt0) REVERT: A 3873 GLU cc_start: 0.7103 (tp30) cc_final: 0.6788 (tm-30) REVERT: A 4050 LYS cc_start: 0.7079 (tttt) cc_final: 0.6493 (tptt) REVERT: A 4203 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7743 (mttt) REVERT: A 4393 MET cc_start: 0.8088 (mmm) cc_final: 0.7880 (tpt) REVERT: A 4548 LYS cc_start: 0.8496 (mptt) cc_final: 0.7936 (mmtt) REVERT: A 4573 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 4577 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7637 (tm-30) outliers start: 19 outliers final: 12 residues processed: 279 average time/residue: 0.1729 time to fit residues: 75.1689 Evaluate side-chains 255 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 2525 ILE Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3277 GLN Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4203 LYS Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [65, 164, 17, 243, 33, 192, 204, 40, 248, 258, 282] chunk 65 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN A3044 ASN A3840 GLN A4038 GLN A4323 ASN A4349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.229947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.186217 restraints weight = 25635.612| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 1.93 r_work: 0.3797 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25173 Z= 0.144 Angle : 0.539 7.673 34126 Z= 0.275 Chirality : 0.041 0.249 3833 Planarity : 0.004 0.052 4352 Dihedral : 7.357 122.957 3336 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.09 % Allowed : 6.77 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 3040 helix: 1.64 (0.13), residues: 1696 sheet: -1.72 (0.34), residues: 233 loop : 0.13 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2337 TYR 0.018 0.001 TYR A2828 PHE 0.025 0.002 PHE A4568 TRP 0.023 0.001 TRP A2286 HIS 0.005 0.001 HIS A1884 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (25173) covalent geometry : angle 0.53874 / 0.27 (34126) hydrogen bonds : bond 0.03924 / 2.52 ( 1340) hydrogen bonds : angle 4.38720 / 3.05 ( 3846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7399 (mmt) cc_final: 0.6915 (mtm) REVERT: A 1593 ASP cc_start: 0.7101 (t0) cc_final: 0.6651 (m-30) REVERT: A 2504 GLN cc_start: 0.7213 (tt0) cc_final: 0.6886 (tm-30) REVERT: A 2505 TYR cc_start: 0.6622 (m-80) cc_final: 0.5838 (m-80) REVERT: A 2591 GLU cc_start: 0.7289 (pt0) cc_final: 0.6832 (mt-10) REVERT: A 2630 LYS cc_start: 0.7187 (mttp) cc_final: 0.6792 (mttp) REVERT: A 2648 ILE cc_start: 0.7936 (mm) cc_final: 0.7725 (mm) REVERT: A 2752 ASP cc_start: 0.7217 (t0) cc_final: 0.6407 (m-30) REVERT: A 2753 LYS cc_start: 0.8005 (tptp) cc_final: 0.7720 (tptp) REVERT: A 3027 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7019 (mtt90) REVERT: A 3615 ARG cc_start: 0.7555 (tpm170) cc_final: 0.6515 (mtm-85) REVERT: A 3873 GLU cc_start: 0.7049 (tp30) cc_final: 0.6750 (tm-30) REVERT: A 3983 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8346 (mt) REVERT: A 4050 LYS cc_start: 0.7104 (tttt) cc_final: 0.6517 (tptt) REVERT: A 4393 MET cc_start: 0.8086 (mmm) cc_final: 0.7864 (tpt) REVERT: A 4434 GLN cc_start: 0.6429 (mp-120) cc_final: 0.6180 (tm-30) REVERT: A 4513 ILE cc_start: 0.7437 (mt) cc_final: 0.7186 (mt) REVERT: A 4548 LYS cc_start: 0.8475 (mptt) cc_final: 0.7906 (mmtt) REVERT: A 4573 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 4577 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7542 (tm-30) outliers start: 30 outliers final: 20 residues processed: 275 average time/residue: 0.1713 time to fit residues: 73.5156 Evaluate side-chains 262 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2525 ILE Chi-restraints excluded: chain A residue 2636 VAL Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3277 GLN Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3803 LYS Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [194, 211, 213, 163, 134, 112, 131, 2, 170, 198, 93] chunk 194 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 GLN A4349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.277728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.221670 restraints weight = 27228.347| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.45 r_work: 0.3756 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 25173 Z= 0.213 Angle : 0.600 8.119 34126 Z= 0.305 Chirality : 0.043 0.249 3833 Planarity : 0.005 0.054 4352 Dihedral : 7.331 118.057 3336 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 8.23 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 3040 helix: 1.46 (0.13), residues: 1688 sheet: -1.89 (0.33), residues: 232 loop : 0.02 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2384 TYR 0.022 0.002 TYR A3233 PHE 0.027 0.002 PHE A3898 TRP 0.023 0.002 TRP A2286 HIS 0.009 0.001 HIS A1877 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.21 (25173) covalent geometry : angle 0.60024 / 0.31 (34126) hydrogen bonds : bond 0.04202 / 2.71 ( 1340) hydrogen bonds : angle 4.51516 / 3.13 ( 3846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7670 (mmt) cc_final: 0.7070 (mtm) REVERT: A 1582 LYS cc_start: 0.8265 (mmmt) cc_final: 0.8021 (mmmt) REVERT: A 1593 ASP cc_start: 0.7169 (t0) cc_final: 0.6708 (m-30) REVERT: A 2064 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7228 (m-40) REVERT: A 2504 GLN cc_start: 0.7298 (tt0) cc_final: 0.6975 (tm-30) REVERT: A 2505 TYR cc_start: 0.6726 (m-80) cc_final: 0.5967 (m-80) REVERT: A 2591 GLU cc_start: 0.7354 (pt0) cc_final: 0.6881 (mt-10) REVERT: A 2630 LYS cc_start: 0.7155 (mttp) cc_final: 0.6750 (mttp) REVERT: A 2648 ILE cc_start: 0.8032 (mm) cc_final: 0.7787 (mm) REVERT: A 2689 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7723 (mtm-85) REVERT: A 2752 ASP cc_start: 0.7321 (t0) cc_final: 0.6577 (m-30) REVERT: A 2753 LYS cc_start: 0.8049 (tptp) cc_final: 0.7757 (tptp) REVERT: A 2781 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7722 (mt) REVERT: A 2988 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 3018 SER cc_start: 0.8899 (t) cc_final: 0.8620 (m) REVERT: A 3027 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7040 (mtt90) REVERT: A 3109 MET cc_start: 0.3300 (mtt) cc_final: 0.2970 (mtt) REVERT: A 3615 ARG cc_start: 0.7662 (tpm170) cc_final: 0.6553 (mtm-85) REVERT: A 3800 GLU cc_start: 0.8249 (tp30) cc_final: 0.7659 (tt0) REVERT: A 3873 GLU cc_start: 0.7081 (tp30) cc_final: 0.6815 (tm-30) REVERT: A 3983 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 4050 LYS cc_start: 0.7134 (tttt) cc_final: 0.6571 (tptt) REVERT: A 4434 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: A 4513 ILE cc_start: 0.7652 (mt) cc_final: 0.7432 (mt) REVERT: A 4548 LYS cc_start: 0.8470 (mptt) cc_final: 0.7935 (mmtt) REVERT: A 4573 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 4577 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7532 (tm-30) outliers start: 52 outliers final: 32 residues processed: 280 average time/residue: 0.1679 time to fit residues: 73.8146 Evaluate side-chains 277 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 2014 VAL Chi-restraints excluded: chain A residue 2064 ASN Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2525 ILE Chi-restraints excluded: chain A residue 2527 ASP Chi-restraints excluded: chain A residue 2636 VAL Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3277 GLN Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3602 ILE Chi-restraints excluded: chain A residue 3624 VAL Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3788 VAL Chi-restraints excluded: chain A residue 3803 LYS Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4434 GLN Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [81, 32, 268, 146, 107, 184, 17, 22, 299, 36, 9] chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 268 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 299 optimal weight: 7.9990 chunk 36 optimal weight: 0.0030 chunk 9 optimal weight: 0.4980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN A3033 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 GLN A4323 ASN A4349 ASN A4434 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.233445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198896 restraints weight = 25690.792| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 1.69 r_work: 0.3924 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25173 Z= 0.106 Angle : 0.507 7.526 34126 Z= 0.258 Chirality : 0.039 0.271 3833 Planarity : 0.004 0.052 4352 Dihedral : 7.099 123.351 3336 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.38 % Allowed : 9.79 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 3040 helix: 1.79 (0.13), residues: 1683 sheet: -1.85 (0.33), residues: 232 loop : 0.14 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2030 TYR 0.020 0.001 TYR A3897 PHE 0.022 0.001 PHE A2596 TRP 0.027 0.001 TRP A2286 HIS 0.004 0.001 HIS A1800 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (25173) covalent geometry : angle 0.50664 / 0.26 (34126) hydrogen bonds : bond 0.03527 / 2.27 ( 1340) hydrogen bonds : angle 4.17107 / 2.89 ( 3846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7390 (mmt) cc_final: 0.6988 (mtm) REVERT: A 1593 ASP cc_start: 0.7216 (t0) cc_final: 0.6798 (m-30) REVERT: A 1709 ILE cc_start: 0.7677 (mt) cc_final: 0.7428 (mm) REVERT: A 1910 MET cc_start: 0.8605 (ttt) cc_final: 0.8338 (ttt) REVERT: A 2591 GLU cc_start: 0.7079 (pt0) cc_final: 0.6861 (mt-10) REVERT: A 2630 LYS cc_start: 0.7035 (mttp) cc_final: 0.6682 (mttp) REVERT: A 2752 ASP cc_start: 0.7061 (t0) cc_final: 0.6588 (m-30) REVERT: A 2753 LYS cc_start: 0.8020 (tptp) cc_final: 0.7762 (tptp) REVERT: A 3027 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7183 (mtt90) REVERT: A 3109 MET cc_start: 0.3099 (mtt) cc_final: 0.2763 (mtt) REVERT: A 3190 ARG cc_start: 0.7449 (mtt180) cc_final: 0.7237 (ttp-170) REVERT: A 3615 ARG cc_start: 0.7343 (tpm170) cc_final: 0.6491 (mtm-85) REVERT: A 3800 GLU cc_start: 0.7838 (tp30) cc_final: 0.7595 (tt0) REVERT: A 3873 GLU cc_start: 0.6922 (tp30) cc_final: 0.6714 (tm-30) REVERT: A 3983 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 4015 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6252 (p) REVERT: A 4050 LYS cc_start: 0.7107 (tttt) cc_final: 0.6608 (tptt) REVERT: A 4203 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7841 (mttt) REVERT: A 4434 GLN cc_start: 0.6596 (mp10) cc_final: 0.6296 (tm-30) REVERT: A 4548 LYS cc_start: 0.8372 (mptt) cc_final: 0.7924 (mmtt) REVERT: A 4561 LEU cc_start: 0.8116 (tp) cc_final: 0.7791 (tp) REVERT: A 4573 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 4577 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7501 (tm-30) outliers start: 38 outliers final: 23 residues processed: 286 average time/residue: 0.1701 time to fit residues: 77.1266 Evaluate side-chains 269 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2064 ASN Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3144 VAL Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4203 LYS Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4675 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [43, 22, 41, 0, 269, 283, 129, 238, 224, 50, 69] chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 60.0000 chunk 269 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 238 optimal weight: 0.0980 chunk 224 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 GLN A4323 ASN A4349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.248273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178597 restraints weight = 27044.808| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.07 r_work: 0.3721 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25173 Z= 0.129 Angle : 0.519 7.678 34126 Z= 0.263 Chirality : 0.040 0.175 3833 Planarity : 0.004 0.052 4352 Dihedral : 7.036 122.959 3336 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.64 % Allowed : 10.34 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 3040 helix: 1.82 (0.13), residues: 1680 sheet: -1.86 (0.33), residues: 232 loop : 0.12 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2030 TYR 0.018 0.001 TYR A2828 PHE 0.020 0.002 PHE A3898 TRP 0.025 0.001 TRP A2286 HIS 0.005 0.001 HIS A1884 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (25173) covalent geometry : angle 0.51927 / 0.26 (34126) hydrogen bonds : bond 0.03602 / 2.31 ( 1340) hydrogen bonds : angle 4.17246 / 2.89 ( 3846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7044 (mmt) cc_final: 0.6516 (mtm) REVERT: A 1593 ASP cc_start: 0.6835 (t0) cc_final: 0.6276 (m-30) REVERT: A 1709 ILE cc_start: 0.7534 (mt) cc_final: 0.7311 (mm) REVERT: A 2591 GLU cc_start: 0.7081 (pt0) cc_final: 0.6422 (mt-10) REVERT: A 2613 LEU cc_start: 0.7678 (tp) cc_final: 0.7457 (tp) REVERT: A 2626 LEU cc_start: 0.6773 (mp) cc_final: 0.6552 (mt) REVERT: A 2630 LYS cc_start: 0.7106 (mttp) cc_final: 0.6701 (mttp) REVERT: A 2752 ASP cc_start: 0.6824 (t0) cc_final: 0.6050 (m-30) REVERT: A 2753 LYS cc_start: 0.7756 (tptp) cc_final: 0.7440 (tptp) REVERT: A 3027 ARG cc_start: 0.7662 (mtt90) cc_final: 0.6719 (mtt90) REVERT: A 3109 MET cc_start: 0.3377 (mtt) cc_final: 0.3075 (mtt) REVERT: A 3615 ARG cc_start: 0.7591 (tpm170) cc_final: 0.6314 (mtm-85) REVERT: A 3777 LEU cc_start: 0.7440 (tp) cc_final: 0.7238 (tp) REVERT: A 3800 GLU cc_start: 0.7865 (tp30) cc_final: 0.7213 (tt0) REVERT: A 3873 GLU cc_start: 0.6846 (tp30) cc_final: 0.6516 (tm-30) REVERT: A 3983 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 4015 THR cc_start: 0.6477 (OUTLIER) cc_final: 0.6060 (p) REVERT: A 4203 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7541 (mttt) REVERT: A 4365 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 4434 GLN cc_start: 0.6384 (mp10) cc_final: 0.5818 (tm-30) REVERT: A 4548 LYS cc_start: 0.8446 (mptt) cc_final: 0.7716 (mmtt) REVERT: A 4561 LEU cc_start: 0.7731 (tp) cc_final: 0.7432 (tp) REVERT: A 4572 MET cc_start: 0.7551 (mmp) cc_final: 0.7314 (mmt) REVERT: A 4573 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 4577 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7281 (tm-30) outliers start: 45 outliers final: 27 residues processed: 278 average time/residue: 0.1656 time to fit residues: 73.3002 Evaluate side-chains 272 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2306 MET Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2636 VAL Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2950 ILE Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3694 ILE Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4203 LYS Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [186, 242, 142, 208, 197, 189, 111, 274, 131, 207, 211] chunk 186 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 207 optimal weight: 0.0020 chunk 211 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN A4038 GLN A4349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.232832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.196807 restraints weight = 25723.939| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.67 r_work: 0.3954 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25173 Z= 0.119 Angle : 0.510 7.590 34126 Z= 0.259 Chirality : 0.040 0.172 3833 Planarity : 0.004 0.054 4352 Dihedral : 6.965 123.252 3336 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.57 % Allowed : 10.59 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 3040 helix: 1.86 (0.13), residues: 1680 sheet: -1.87 (0.33), residues: 231 loop : 0.13 (0.20), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2030 TYR 0.023 0.001 TYR A3233 PHE 0.019 0.001 PHE A4568 TRP 0.024 0.001 TRP A2286 HIS 0.004 0.001 HIS A3772 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (25173) covalent geometry : angle 0.51043 / 0.26 (34126) hydrogen bonds : bond 0.03526 / 2.26 ( 1340) hydrogen bonds : angle 4.13337 / 2.86 ( 3846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.7473 (mmt) cc_final: 0.7056 (mtm) REVERT: A 1593 ASP cc_start: 0.7320 (t0) cc_final: 0.6910 (m-30) REVERT: A 1709 ILE cc_start: 0.7635 (mt) cc_final: 0.7416 (mm) REVERT: A 2613 LEU cc_start: 0.7862 (tp) cc_final: 0.7613 (tp) REVERT: A 2626 LEU cc_start: 0.7630 (mp) cc_final: 0.7373 (mt) REVERT: A 2630 LYS cc_start: 0.7032 (mttp) cc_final: 0.6701 (mttp) REVERT: A 2752 ASP cc_start: 0.6904 (t0) cc_final: 0.6579 (m-30) REVERT: A 3027 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7188 (mtt90) REVERT: A 3109 MET cc_start: 0.3243 (mtt) cc_final: 0.2916 (mtt) REVERT: A 3615 ARG cc_start: 0.7471 (tpm170) cc_final: 0.6489 (mtm-85) REVERT: A 3777 LEU cc_start: 0.7779 (tp) cc_final: 0.7562 (tp) REVERT: A 3983 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 4015 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6291 (p) REVERT: A 4203 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7985 (mttt) REVERT: A 4365 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 4434 GLN cc_start: 0.6531 (mp10) cc_final: 0.6322 (tm-30) REVERT: A 4548 LYS cc_start: 0.8285 (mptt) cc_final: 0.7926 (mmtt) REVERT: A 4561 LEU cc_start: 0.8150 (tp) cc_final: 0.7824 (tp) REVERT: A 4573 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 4577 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7557 (tm-30) outliers start: 43 outliers final: 32 residues processed: 276 average time/residue: 0.1719 time to fit residues: 75.0542 Evaluate side-chains 275 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2306 MET Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2636 VAL Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2950 ILE Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3602 ILE Chi-restraints excluded: chain A residue 3624 VAL Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3694 ILE Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4162 ILE Chi-restraints excluded: chain A residue 4203 LYS Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4675 ASP Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [264, 148, 36, 128, 71, 39, 288, 113, 142, 242, 292] chunk 264 optimal weight: 0.0370 chunk 148 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 242 optimal weight: 0.5980 chunk 292 optimal weight: 0.8980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1590 HIS A1962 GLN A2229 GLN A2700 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 GLN A4349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.249306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.4115 r_free = 0.4115 target = 0.181894 restraints weight = 27078.378| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.23 r_work: 0.3764 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25173 Z= 0.118 Angle : 0.512 7.441 34126 Z= 0.260 Chirality : 0.040 0.200 3833 Planarity : 0.004 0.054 4352 Dihedral : 6.915 123.830 3336 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 10.67 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 3040 helix: 1.86 (0.13), residues: 1689 sheet: -1.87 (0.34), residues: 231 loop : 0.12 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2030 TYR 0.024 0.001 TYR A3233 PHE 0.028 0.001 PHE A2596 TRP 0.024 0.001 TRP A2286 HIS 0.004 0.001 HIS A4205 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25173) covalent geometry : angle 0.51234 / 0.26 (34126) hydrogen bonds : bond 0.03496 / 2.23 ( 1340) hydrogen bonds : angle 4.11442 / 2.84 ( 3846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1577 MET cc_start: 0.6978 (mmt) cc_final: 0.6516 (mtm) REVERT: A 1593 ASP cc_start: 0.6910 (t0) cc_final: 0.6371 (m-30) REVERT: A 1700 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7057 (m) REVERT: A 1709 ILE cc_start: 0.7553 (mt) cc_final: 0.7334 (mm) REVERT: A 1910 MET cc_start: 0.8746 (ttt) cc_final: 0.8426 (ttt) REVERT: A 2269 ASN cc_start: 0.6750 (m110) cc_final: 0.6514 (m110) REVERT: A 2613 LEU cc_start: 0.7702 (tp) cc_final: 0.7453 (tp) REVERT: A 2626 LEU cc_start: 0.6786 (mp) cc_final: 0.6577 (mt) REVERT: A 2630 LYS cc_start: 0.7103 (mttp) cc_final: 0.6696 (mttp) REVERT: A 2748 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6649 (mp) REVERT: A 2752 ASP cc_start: 0.6724 (t0) cc_final: 0.5964 (m-30) REVERT: A 3027 ARG cc_start: 0.7662 (mtt90) cc_final: 0.6755 (mtt90) REVERT: A 3109 MET cc_start: 0.3391 (mtt) cc_final: 0.3080 (mtt) REVERT: A 3195 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8119 (mt-10) REVERT: A 3615 ARG cc_start: 0.7558 (tpm170) cc_final: 0.6305 (mtm-85) REVERT: A 3777 LEU cc_start: 0.7516 (tp) cc_final: 0.7314 (tp) REVERT: A 3983 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 4015 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6131 (p) REVERT: A 4365 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 4434 GLN cc_start: 0.6409 (mp10) cc_final: 0.5880 (tm-30) REVERT: A 4548 LYS cc_start: 0.8434 (mptt) cc_final: 0.7734 (mmtt) REVERT: A 4561 LEU cc_start: 0.7813 (tp) cc_final: 0.7518 (tp) REVERT: A 4573 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 4577 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7344 (tm-30) outliers start: 50 outliers final: 38 residues processed: 275 average time/residue: 0.1665 time to fit residues: 72.1216 Evaluate side-chains 278 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1700 VAL Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2306 MET Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2527 ASP Chi-restraints excluded: chain A residue 2636 VAL Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2748 LEU Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2950 ILE Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3602 ILE Chi-restraints excluded: chain A residue 3624 VAL Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4162 ILE Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4323 ASN Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4675 ASP Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [55, 135, 279, 41, 181, 205, 130, 183, 93, 289, 81] chunk 55 optimal weight: 0.0670 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1962 GLN A2229 GLN A2700 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.234926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.196398 restraints weight = 25741.983| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.65 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25173 Z= 0.101 Angle : 0.500 7.311 34126 Z= 0.254 Chirality : 0.039 0.195 3833 Planarity : 0.004 0.054 4352 Dihedral : 6.811 124.665 3336 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.46 % Allowed : 11.36 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 3040 helix: 1.94 (0.13), residues: 1689 sheet: -1.80 (0.34), residues: 231 loop : 0.19 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3620 TYR 0.017 0.001 TYR A3897 PHE 0.016 0.001 PHE A3898 TRP 0.035 0.001 TRP A4564 HIS 0.004 0.001 HIS A4205 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (25173) covalent geometry : angle 0.50004 / 0.25 (34126) hydrogen bonds : bond 0.03333 / 2.13 ( 1340) hydrogen bonds : angle 4.03412 / 2.79 ( 3846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2352 TRP cc_start: 0.6738 (m-10) cc_final: 0.6535 (m-10) REVERT: A 2613 LEU cc_start: 0.7767 (tp) cc_final: 0.7535 (tp) REVERT: A 2626 LEU cc_start: 0.7812 (mp) cc_final: 0.7537 (mt) REVERT: A 2630 LYS cc_start: 0.6650 (mttp) cc_final: 0.6387 (mttp) REVERT: A 2748 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6512 (mp) REVERT: A 3027 ARG cc_start: 0.7381 (mtt90) cc_final: 0.7022 (mtt90) REVERT: A 3109 MET cc_start: 0.2916 (mtt) cc_final: 0.2566 (mtt) REVERT: A 3615 ARG cc_start: 0.7070 (tpm170) cc_final: 0.6368 (mtm-85) REVERT: A 3729 VAL cc_start: 0.7486 (t) cc_final: 0.7201 (p) REVERT: A 3983 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8207 (mt) REVERT: A 4015 THR cc_start: 0.6597 (OUTLIER) cc_final: 0.6305 (p) REVERT: A 4365 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 4393 MET cc_start: 0.7868 (tpt) cc_final: 0.7171 (tpt) REVERT: A 4434 GLN cc_start: 0.6593 (mp10) cc_final: 0.6372 (tm-30) REVERT: A 4561 LEU cc_start: 0.7944 (tp) cc_final: 0.7650 (tp) REVERT: A 4577 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7300 (tm-30) outliers start: 40 outliers final: 29 residues processed: 271 average time/residue: 0.1625 time to fit residues: 69.7823 Evaluate side-chains 268 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2306 MET Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2748 LEU Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2950 ILE Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3694 ILE Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3879 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4323 ASN Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4408 LEU Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [252, 224, 282, 132, 250, 238, 82, 121, 63, 140, 24] chunk 252 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 238 optimal weight: 0.1980 chunk 82 optimal weight: 0.0770 chunk 121 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN A3140 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4073 GLN A4263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.233431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.194782 restraints weight = 25779.769| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.75 r_work: 0.3852 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25173 Z= 0.101 Angle : 0.503 7.227 34126 Z= 0.255 Chirality : 0.039 0.191 3833 Planarity : 0.004 0.054 4352 Dihedral : 6.619 124.372 3336 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.27 % Allowed : 11.61 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 3040 helix: 1.93 (0.13), residues: 1700 sheet: -1.81 (0.33), residues: 242 loop : 0.24 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3620 TYR 0.016 0.001 TYR A2828 PHE 0.021 0.001 PHE A2596 TRP 0.052 0.001 TRP A4564 HIS 0.004 0.001 HIS A4205 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (25173) covalent geometry : angle 0.50255 / 0.25 (34126) hydrogen bonds : bond 0.03327 / 2.12 ( 1340) hydrogen bonds : angle 3.98275 / 2.75 ( 3846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2352 TRP cc_start: 0.6946 (m-10) cc_final: 0.6718 (m-10) REVERT: A 2591 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7065 (mp0) REVERT: A 2613 LEU cc_start: 0.7734 (tp) cc_final: 0.7501 (tp) REVERT: A 2626 LEU cc_start: 0.7461 (mp) cc_final: 0.7223 (mt) REVERT: A 2630 LYS cc_start: 0.7050 (mttp) cc_final: 0.6722 (mttp) REVERT: A 2748 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6930 (mp) REVERT: A 3027 ARG cc_start: 0.7701 (mtt90) cc_final: 0.6988 (mtt90) REVERT: A 3109 MET cc_start: 0.3348 (mtt) cc_final: 0.3007 (mtt) REVERT: A 3585 MET cc_start: 0.9122 (tpp) cc_final: 0.8889 (mmp) REVERT: A 3614 MET cc_start: 0.8270 (tpp) cc_final: 0.7999 (tpt) REVERT: A 3615 ARG cc_start: 0.7671 (tpm170) cc_final: 0.6553 (mtm-85) REVERT: A 3669 ASN cc_start: 0.7960 (t0) cc_final: 0.7699 (t0) REVERT: A 3729 VAL cc_start: 0.7572 (t) cc_final: 0.7246 (p) REVERT: A 3880 SER cc_start: 0.7691 (t) cc_final: 0.7193 (m) REVERT: A 3983 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 4015 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.6265 (p) REVERT: A 4365 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (p) REVERT: A 4393 MET cc_start: 0.7988 (tpt) cc_final: 0.7248 (tpt) REVERT: A 4434 GLN cc_start: 0.6504 (mp10) cc_final: 0.6158 (tm-30) REVERT: A 4561 LEU cc_start: 0.8171 (tp) cc_final: 0.7831 (tp) REVERT: A 4577 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7671 (tm-30) outliers start: 35 outliers final: 30 residues processed: 266 average time/residue: 0.1742 time to fit residues: 74.4530 Evaluate side-chains 268 residues out of total 2747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1881 GLU Chi-restraints excluded: chain A residue 2306 MET Chi-restraints excluded: chain A residue 2421 LEU Chi-restraints excluded: chain A residue 2422 THR Chi-restraints excluded: chain A residue 2645 ASP Chi-restraints excluded: chain A residue 2646 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2748 LEU Chi-restraints excluded: chain A residue 2816 VAL Chi-restraints excluded: chain A residue 2950 ILE Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 3072 ILE Chi-restraints excluded: chain A residue 3160 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3642 GLU Chi-restraints excluded: chain A residue 3694 ILE Chi-restraints excluded: chain A residue 3752 GLN Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3879 ILE Chi-restraints excluded: chain A residue 3937 ASN Chi-restraints excluded: chain A residue 3983 ILE Chi-restraints excluded: chain A residue 4015 THR Chi-restraints excluded: chain A residue 4034 VAL Chi-restraints excluded: chain A residue 4086 MET Chi-restraints excluded: chain A residue 4232 MET Chi-restraints excluded: chain A residue 4323 ASN Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4408 LEU Chi-restraints excluded: chain A residue 4555 VAL Chi-restraints excluded: chain A residue 4616 LEU Chi-restraints excluded: chain A residue 4682 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [79, 232, 74, 110, 281, 178, 167, 15, 224, 235, 251] chunk 79 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 281 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2229 GLN A2700 ASN ** A3772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.228530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.184106 restraints weight = 25565.691| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.94 r_work: 0.3773 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25173 Z= 0.116 Angle : 0.515 7.219 34126 Z= 0.260 Chirality : 0.040 0.194 3833 Planarity : 0.004 0.054 4352 Dihedral : 6.512 122.755 3336 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.35 % Allowed : 11.90 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 3040 helix: 1.94 (0.13), residues: 1693 sheet: -1.73 (0.34), residues: 230 loop : 0.18 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3620 TYR 0.016 0.001 TYR A2828 PHE 0.042 0.001 PHE A2762 TRP 0.044 0.001 TRP A4564 HIS 0.005 0.001 HIS A4205 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25173) covalent geometry : angle 0.51498 / 0.26 (34126) hydrogen bonds : bond 0.03360 / 2.15 ( 1340) hydrogen bonds : angle 4.00444 / 2.76 ( 3846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.87 seconds wall clock time: 93 minutes 54.25 seconds (5634.25 seconds total)