Starting phenix.real_space_refine on Fri Jun 20 10:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn6_44723/06_2025/9bn6_44723.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.040 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 115 5.16 5 C 14683 2.51 5 N 3983 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23078 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2855, 22962 Classifications: {'peptide': 2855} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 129, 'TRANS': 2725} Chain breaks: 6 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.74, per 1000 atoms: 0.55 Number of scatterers: 23078 At special positions: 0 Unit cell: (126.873, 169.164, 152.019, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 10 15.00 O 4287 8.00 N 3983 7.00 C 14683 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: 5.17 Conformation dependent library (CDL) restraints added in 2.6 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 20 sheets defined 62.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 1463 through 1470 Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.883A pdb=" N LYS A1496 " --> pdb=" O ASP A1492 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL A1497 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1554 removed outlier: 4.046A pdb=" N LEU A1521 " --> pdb=" O GLU A1517 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.512A pdb=" N THR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.663A pdb=" N VAL A1591 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1592 " --> pdb=" O VAL A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1658 removed outlier: 3.737A pdb=" N LEU A1650 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A1652 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS A1655 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYS A1656 " --> pdb=" O LYS A1652 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.881A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1776 through 1798 removed outlier: 3.806A pdb=" N SER A1780 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1825 removed outlier: 3.535A pdb=" N THR A1822 " --> pdb=" O GLN A1818 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 removed outlier: 3.659A pdb=" N GLN A1855 " --> pdb=" O ASP A1852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1852 through 1855' Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 4.003A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.638A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 removed outlier: 3.542A pdb=" N LYS A2033 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2077 removed outlier: 3.513A pdb=" N LEU A2065 " --> pdb=" O THR A2061 " (cutoff:3.500A) Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.753A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 3.990A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.527A pdb=" N GLU A2180 " --> pdb=" O THR A2176 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2289 Processing helix chain 'A' and resid 2308 through 2320 removed outlier: 5.303A pdb=" N ASN A2314 " --> pdb=" O GLU A2310 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.712A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.571A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2443 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.852A pdb=" N LEU A2458 " --> pdb=" O CYS A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2502 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.505A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.913A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2601 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.979A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.934A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 4.080A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2783 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 4.221A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A2800 " --> pdb=" O PRO A2796 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2886 through 2904 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3013 removed outlier: 3.671A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 removed outlier: 4.160A pdb=" N PHE A3021 " --> pdb=" O PRO A3018 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3111 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.630A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3502 removed outlier: 3.696A pdb=" N ALA A3477 " --> pdb=" O ASN A3473 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3504 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.742A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.717A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3736 removed outlier: 3.599A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 Processing helix chain 'A' and resid 3763 through 3786 removed outlier: 4.112A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3801 Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.787A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.587A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.506A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3873 removed outlier: 3.937A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3911 through 3914 Processing helix chain 'A' and resid 3928 through 3941 removed outlier: 3.794A pdb=" N LEU A3941 " --> pdb=" O ARG A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.655A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.938A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.719A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.907A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.849A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.764A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 removed outlier: 3.551A pdb=" N LYS A4171 " --> pdb=" O SER A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4194 through 4196 No H-bonds generated for 'chain 'A' and resid 4194 through 4196' Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4251 through 4256 removed outlier: 4.239A pdb=" N ARG A4255 " --> pdb=" O ILE A4251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A4256 " --> pdb=" O TYR A4252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4251 through 4256' Processing helix chain 'A' and resid 4258 through 4273 removed outlier: 3.548A pdb=" N GLN A4262 " --> pdb=" O ASN A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.793A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4345 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4405 removed outlier: 3.537A pdb=" N ILE A4405 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4440 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.908A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4500 through 4507 Processing helix chain 'A' and resid 4516 through 4531 Processing helix chain 'A' and resid 4532 through 4534 No H-bonds generated for 'chain 'A' and resid 4532 through 4534' Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4639 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1479 Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 4.326A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 3.703A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.490A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 removed outlier: 3.524A pdb=" N VAL A2006 " --> pdb=" O CYS A1999 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2325 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 6.252A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP A2664 " --> pdb=" O VAL A2618 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU A2620 " --> pdb=" O ASP A2664 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 4.133A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2872 through 2873 removed outlier: 4.603A pdb=" N LEU A2872 " --> pdb=" O VAL A2884 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.052A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.317A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 3661 through 3662 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 3.513A pdb=" N THR A4067 " --> pdb=" O TRP A4093 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4285 through 4288 removed outlier: 5.886A pdb=" N CYS A4286 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A4294 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4539 through 4545 Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.941A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.66 Time building geometry restraints manager: 6.25 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: 7564 1.34 - 1.46: 5055 1.46 - 1.58: 10753 1.58 - 1.70: 14 1.70 - 1.82: 192 Bond restraints: 23578 Sorted by residual: bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.330 1.361 -0.030 1.19e-02 7.06e+03 6.51e+00 bond pdb=" C SER A4172 " pdb=" N PRO A4173 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.33e-02 5.65e+03 2.82e+00 bond pdb=" CA GLY A2196 " pdb=" C GLY A2196 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.53e+00 bond pdb=" CG MET A2779 " pdb=" SD MET A2779 " ideal model delta sigma weight residual 1.803 1.767 0.036 2.50e-02 1.60e+03 2.06e+00 bond pdb=" N GLY A2196 " pdb=" CA GLY A2196 " ideal model delta sigma weight residual 1.464 1.450 0.015 1.12e-02 7.97e+03 1.68e+00 ... (remaining 23573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 31274 1.75 - 3.50: 593 3.50 - 5.24: 85 5.24 - 6.99: 28 6.99 - 8.74: 5 Bond angle restraints: 31985 Sorted by residual: angle pdb=" N MET A2867 " pdb=" CA MET A2867 " pdb=" C MET A2867 " ideal model delta sigma weight residual 114.62 107.72 6.90 1.14e+00 7.69e-01 3.66e+01 angle pdb=" CA MET A2867 " pdb=" C MET A2867 " pdb=" N SER A2868 " ideal model delta sigma weight residual 119.71 115.30 4.41 1.17e+00 7.31e-01 1.42e+01 angle pdb=" N MET A2779 " pdb=" CA MET A2779 " pdb=" CB MET A2779 " ideal model delta sigma weight residual 110.12 115.55 -5.43 1.47e+00 4.63e-01 1.37e+01 angle pdb=" N GLN A3751 " pdb=" CA GLN A3751 " pdb=" CB GLN A3751 " ideal model delta sigma weight residual 110.28 115.94 -5.66 1.55e+00 4.16e-01 1.34e+01 angle pdb=" C THR A4033 " pdb=" N GLU A4034 " pdb=" CA GLU A4034 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 ... (remaining 31980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 13305 21.64 - 43.28: 868 43.28 - 64.92: 99 64.92 - 86.56: 31 86.56 - 108.20: 3 Dihedral angle restraints: 14306 sinusoidal: 5944 harmonic: 8362 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 48.20 -108.20 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" CA ALA A2866 " pdb=" C ALA A2866 " pdb=" N MET A2867 " pdb=" CA MET A2867 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA THR A2144 " pdb=" C THR A2144 " pdb=" N MET A2145 " pdb=" CA MET A2145 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 14303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2850 0.046 - 0.092: 600 0.092 - 0.138: 142 0.138 - 0.183: 5 0.183 - 0.229: 3 Chirality restraints: 3600 Sorted by residual: chirality pdb=" CB ILE A2759 " pdb=" CA ILE A2759 " pdb=" CG1 ILE A2759 " pdb=" CG2 ILE A2759 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA MET A3126 " pdb=" N MET A3126 " pdb=" C MET A3126 " pdb=" CB MET A3126 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A3677 " pdb=" CA ILE A3677 " pdb=" CG1 ILE A3677 " pdb=" CG2 ILE A3677 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3597 not shown) Planarity restraints: 4087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A3907 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C HIS A3907 " -0.034 2.00e-02 2.50e+03 pdb=" O HIS A3907 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A3908 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2584 " -0.012 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP A2584 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A2584 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A2584 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A2584 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A2584 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2584 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2584 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2584 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A2584 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2845 " 0.013 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" CG TRP A2845 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A2845 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A2845 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A2845 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2845 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A2845 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2845 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2845 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A2845 " 0.001 2.00e-02 2.50e+03 ... (remaining 4084 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 438 2.69 - 3.25: 24167 3.25 - 3.80: 38539 3.80 - 4.35: 49695 4.35 - 4.90: 80146 Nonbonded interactions: 192985 Sorted by model distance: nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU A3898 " pdb=" OG1 THR A3981 " model vdw 2.160 3.040 nonbonded pdb=" OE2 GLU A3040 " pdb=" NE1 TRP A3053 " model vdw 2.181 3.120 nonbonded pdb=" OG1 THR A2785 " pdb=" OD1 ASP A2787 " model vdw 2.200 3.040 nonbonded pdb=" ND2 ASN A4326 " pdb=" O ASN A4579 " model vdw 2.214 3.120 ... (remaining 192980 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=0.00 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: 2.850 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 55.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23578 Z= 0.135 Angle : 0.607 8.741 31985 Z= 0.331 Chirality : 0.039 0.229 3600 Planarity : 0.004 0.052 4087 Dihedral : 13.810 108.199 8872 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2841 helix: 1.95 (0.13), residues: 1568 sheet: -1.08 (0.33), residues: 246 loop : -0.76 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A2845 HIS 0.004 0.001 HIS A1817 PHE 0.014 0.001 PHE A3813 TYR 0.025 0.001 TYR A2748 ARG 0.009 0.000 ARG A1806 Details of bonding type rmsd hydrogen bonds : bond 0.14009 ( 1309) hydrogen bonds : angle 5.48766 ( 3825) covalent geometry : bond 0.00269 (23578) covalent geometry : angle 0.60719 (31985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.6537 (ttpp) cc_final: 0.5895 (mttt) REVERT: A 1542 ARG cc_start: 0.6910 (mmt90) cc_final: 0.6654 (mmt-90) REVERT: A 1621 ARG cc_start: 0.6961 (ttp-170) cc_final: 0.6731 (ttp-170) REVERT: A 1969 SER cc_start: 0.8552 (t) cc_final: 0.7968 (m) REVERT: A 2347 ASP cc_start: 0.7439 (t0) cc_final: 0.7084 (t0) REVERT: A 2349 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8045 (ptpp) REVERT: A 2485 GLN cc_start: 0.7702 (tt0) cc_final: 0.7269 (tt0) REVERT: A 2487 GLU cc_start: 0.8353 (tt0) cc_final: 0.7775 (tt0) REVERT: A 2603 MET cc_start: 0.6340 (mmp) cc_final: 0.6022 (mmm) REVERT: A 2839 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7196 (tt0) REVERT: A 2845 TRP cc_start: 0.7574 (t-100) cc_final: 0.7251 (t60) REVERT: A 2898 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7630 (mtmm) REVERT: A 3048 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7826 (tp30) REVERT: A 3053 TRP cc_start: 0.6851 (t60) cc_final: 0.6528 (t-100) REVERT: A 3056 SER cc_start: 0.7305 (t) cc_final: 0.7005 (p) REVERT: A 3121 ILE cc_start: 0.7994 (mm) cc_final: 0.7505 (mp) REVERT: A 3497 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7195 (mtpt) REVERT: A 3500 MET cc_start: 0.7870 (tmm) cc_final: 0.7049 (tmm) REVERT: A 3540 ASN cc_start: 0.8922 (t0) cc_final: 0.8222 (t0) REVERT: A 3560 LEU cc_start: 0.8371 (tt) cc_final: 0.8131 (mm) REVERT: A 3685 THR cc_start: 0.8634 (m) cc_final: 0.8284 (t) REVERT: A 3718 LYS cc_start: 0.7413 (ttpt) cc_final: 0.6996 (mtmt) REVERT: A 3799 GLN cc_start: 0.7533 (tp40) cc_final: 0.7329 (tm-30) REVERT: A 3830 GLN cc_start: 0.7242 (tp40) cc_final: 0.7027 (tp40) REVERT: A 3846 LEU cc_start: 0.5662 (mt) cc_final: 0.5276 (mt) REVERT: A 4111 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8646 (mmtt) REVERT: A 4400 ARG cc_start: 0.4703 (tpm170) cc_final: 0.4488 (tpm170) REVERT: A 4410 PHE cc_start: 0.6422 (t80) cc_final: 0.6055 (t80) REVERT: A 4433 ASP cc_start: 0.7088 (t70) cc_final: 0.6826 (t0) REVERT: A 4554 ASP cc_start: 0.7598 (m-30) cc_final: 0.6767 (t0) outliers start: 0 outliers final: 0 residues processed: 572 average time/residue: 0.4354 time to fit residues: 380.1744 Evaluate side-chains 287 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0030 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 0.0010 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 GLN ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN A2689 HIS A2752 ASN A2791 HIS A2857 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3155 HIS A3198 GLN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN A4029 HIS A4079 GLN A4114 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.114782 restraints weight = 44758.943| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.58 r_work: 0.3580 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23578 Z= 0.132 Angle : 0.593 7.533 31985 Z= 0.303 Chirality : 0.040 0.170 3600 Planarity : 0.005 0.061 4087 Dihedral : 6.875 111.832 3193 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 1.10 % Allowed : 9.65 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2841 helix: 2.02 (0.13), residues: 1572 sheet: -1.06 (0.33), residues: 241 loop : -0.68 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A2500 HIS 0.009 0.001 HIS A2588 PHE 0.018 0.001 PHE A3054 TYR 0.020 0.001 TYR A2901 ARG 0.007 0.001 ARG A1628 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1309) hydrogen bonds : angle 4.47074 ( 3825) covalent geometry : bond 0.00290 (23578) covalent geometry : angle 0.59327 (31985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.6467 (ttpp) cc_final: 0.5712 (mttt) REVERT: A 1574 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6615 (tp30) REVERT: A 1621 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6979 (ttp-170) REVERT: A 1637 LEU cc_start: 0.7798 (tt) cc_final: 0.7540 (tt) REVERT: A 1769 MET cc_start: 0.6849 (mmt) cc_final: 0.6465 (mmt) REVERT: A 1969 SER cc_start: 0.8715 (t) cc_final: 0.8248 (m) REVERT: A 2349 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8112 (mtpt) REVERT: A 2603 MET cc_start: 0.6756 (mmp) cc_final: 0.6420 (mmm) REVERT: A 2779 MET cc_start: 0.8160 (mpp) cc_final: 0.7637 (mpp) REVERT: A 2839 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7224 (tt0) REVERT: A 2845 TRP cc_start: 0.7760 (t-100) cc_final: 0.7469 (t60) REVERT: A 2930 GLN cc_start: 0.6285 (mm110) cc_final: 0.6030 (tt0) REVERT: A 3053 TRP cc_start: 0.7369 (t60) cc_final: 0.7015 (t-100) REVERT: A 3056 SER cc_start: 0.7575 (t) cc_final: 0.7192 (p) REVERT: A 3121 ILE cc_start: 0.8197 (mm) cc_final: 0.7916 (mp) REVERT: A 3497 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7855 (mtpt) REVERT: A 3500 MET cc_start: 0.7976 (tmm) cc_final: 0.6962 (tpp) REVERT: A 3540 ASN cc_start: 0.8939 (t0) cc_final: 0.8346 (t0) REVERT: A 3718 LYS cc_start: 0.7330 (ttpt) cc_final: 0.7030 (mtmt) REVERT: A 3751 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6413 (mm110) REVERT: A 3800 GLN cc_start: 0.7298 (tp40) cc_final: 0.7053 (tt0) REVERT: A 4021 MET cc_start: 0.7603 (mmp) cc_final: 0.7269 (mmm) REVERT: A 4111 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8696 (mmtt) REVERT: A 4169 ILE cc_start: 0.8450 (tt) cc_final: 0.8249 (tt) REVERT: A 4422 LYS cc_start: 0.5577 (OUTLIER) cc_final: 0.5148 (tppp) REVERT: A 4554 ASP cc_start: 0.7443 (m-30) cc_final: 0.6651 (t0) outliers start: 28 outliers final: 13 residues processed: 353 average time/residue: 0.4045 time to fit residues: 223.4160 Evaluate side-chains 278 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4422 LYS Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 279 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN A2299 GLN A2918 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3865 GLN A3880 HIS A3912 ASN ** A3985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4566 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.130992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105990 restraints weight = 45380.774| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.57 r_work: 0.3428 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 23578 Z= 0.338 Angle : 0.799 10.027 31985 Z= 0.407 Chirality : 0.048 0.223 3600 Planarity : 0.006 0.059 4087 Dihedral : 7.660 120.601 3193 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer: Outliers : 2.72 % Allowed : 12.20 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2841 helix: 1.18 (0.13), residues: 1593 sheet: -1.39 (0.33), residues: 234 loop : -0.87 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A2500 HIS 0.016 0.002 HIS A2637 PHE 0.030 0.003 PHE A4620 TYR 0.038 0.003 TYR A2748 ARG 0.008 0.001 ARG A1542 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 1309) hydrogen bonds : angle 4.87950 ( 3825) covalent geometry : bond 0.00802 (23578) covalent geometry : angle 0.79925 (31985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1548 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 1574 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6711 (tp30) REVERT: A 1709 MET cc_start: 0.8185 (tmm) cc_final: 0.7864 (ttt) REVERT: A 1769 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: A 1823 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8280 (ttm110) REVERT: A 1966 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: A 1967 MET cc_start: 0.7784 (mmt) cc_final: 0.7286 (mmt) REVERT: A 2189 MET cc_start: 0.8949 (tpp) cc_final: 0.8705 (mtp) REVERT: A 2291 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7175 (t) REVERT: A 2603 MET cc_start: 0.6871 (mmp) cc_final: 0.6504 (mmm) REVERT: A 2654 GLN cc_start: 0.8532 (tp40) cc_final: 0.8310 (tp-100) REVERT: A 2755 MET cc_start: 0.7132 (ttp) cc_final: 0.6694 (ttp) REVERT: A 2882 ILE cc_start: 0.8994 (tt) cc_final: 0.8793 (pt) REVERT: A 3053 TRP cc_start: 0.7299 (t60) cc_final: 0.6830 (t-100) REVERT: A 3497 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7824 (mtpt) REVERT: A 3540 ASN cc_start: 0.8941 (t0) cc_final: 0.8409 (t0) REVERT: A 3718 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7194 (mtmt) REVERT: A 3742 LEU cc_start: 0.6237 (mt) cc_final: 0.4996 (mt) REVERT: A 3743 ARG cc_start: 0.6661 (mmt-90) cc_final: 0.5550 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6447 (mm110) REVERT: A 3800 GLN cc_start: 0.7500 (tp40) cc_final: 0.7295 (tt0) REVERT: A 3816 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: A 3885 MET cc_start: 0.8676 (mmm) cc_final: 0.8337 (mmm) REVERT: A 4111 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8617 (mmtt) REVERT: A 4233 ILE cc_start: 0.8008 (tt) cc_final: 0.7356 (pt) REVERT: A 4422 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5476 (tppp) outliers start: 69 outliers final: 37 residues processed: 318 average time/residue: 0.3744 time to fit residues: 184.8785 Evaluate side-chains 279 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1831 ASP Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1966 ARG Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2683 ILE Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3633 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 GLU Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4422 LYS Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4547 THR Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 224 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 231 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1559 HIS ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1881 GLN A2485 GLN A2621 ASN A2849 ASN ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3880 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110678 restraints weight = 45068.059| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.51 r_work: 0.3515 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23578 Z= 0.132 Angle : 0.579 7.087 31985 Z= 0.296 Chirality : 0.040 0.165 3600 Planarity : 0.004 0.054 4087 Dihedral : 7.020 115.924 3193 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 2.05 % Allowed : 13.90 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 2841 helix: 1.79 (0.13), residues: 1576 sheet: -1.16 (0.34), residues: 226 loop : -0.69 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A2500 HIS 0.005 0.001 HIS A2637 PHE 0.014 0.001 PHE A3908 TYR 0.027 0.001 TYR A3812 ARG 0.005 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 1309) hydrogen bonds : angle 4.32926 ( 3825) covalent geometry : bond 0.00287 (23578) covalent geometry : angle 0.57924 (31985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7154 (mmt-90) cc_final: 0.6678 (tpt170) REVERT: A 1574 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6650 (tp30) REVERT: A 1709 MET cc_start: 0.8090 (tmm) cc_final: 0.7780 (ttt) REVERT: A 1769 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6620 (mmt) REVERT: A 1823 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8323 (ttm110) REVERT: A 1966 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7481 (ttp80) REVERT: A 1969 SER cc_start: 0.8622 (t) cc_final: 0.8126 (m) REVERT: A 2349 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7882 (pttt) REVERT: A 2603 MET cc_start: 0.6744 (mmp) cc_final: 0.6425 (mmm) REVERT: A 2654 GLN cc_start: 0.8599 (tp40) cc_final: 0.8310 (tp-100) REVERT: A 2670 ASP cc_start: 0.7462 (p0) cc_final: 0.7198 (p0) REVERT: A 2752 ASN cc_start: 0.8785 (m-40) cc_final: 0.8482 (m110) REVERT: A 2755 MET cc_start: 0.6921 (ttp) cc_final: 0.6438 (ttp) REVERT: A 2762 LEU cc_start: 0.7740 (mt) cc_final: 0.7505 (mt) REVERT: A 2779 MET cc_start: 0.8115 (mpp) cc_final: 0.7696 (mpp) REVERT: A 2839 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7456 (tt0) REVERT: A 2845 TRP cc_start: 0.7954 (t-100) cc_final: 0.7691 (t-100) REVERT: A 2882 ILE cc_start: 0.8948 (tt) cc_final: 0.8744 (pt) REVERT: A 2930 GLN cc_start: 0.6602 (mm110) cc_final: 0.6141 (tt0) REVERT: A 3053 TRP cc_start: 0.7230 (t60) cc_final: 0.6741 (t-100) REVERT: A 3497 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7897 (mtpt) REVERT: A 3540 ASN cc_start: 0.8976 (t0) cc_final: 0.8507 (t0) REVERT: A 3659 ARG cc_start: 0.5413 (mmm160) cc_final: 0.3947 (tpt-90) REVERT: A 3718 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7316 (mtmm) REVERT: A 3741 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5981 (pmt-80) REVERT: A 3751 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6565 (mm110) REVERT: A 3772 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6496 (p0) REVERT: A 3885 MET cc_start: 0.8561 (mmm) cc_final: 0.8261 (mmm) REVERT: A 4021 MET cc_start: 0.7973 (mmp) cc_final: 0.7589 (mmm) REVERT: A 4107 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6828 (mmm) REVERT: A 4111 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8591 (mmtt) REVERT: A 4157 MET cc_start: 0.8641 (mtp) cc_final: 0.8195 (mtp) REVERT: A 4169 ILE cc_start: 0.8521 (tt) cc_final: 0.8291 (tt) REVERT: A 4233 ILE cc_start: 0.7831 (tt) cc_final: 0.7527 (pt) REVERT: A 4422 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5498 (tppp) outliers start: 52 outliers final: 25 residues processed: 321 average time/residue: 0.3614 time to fit residues: 182.7330 Evaluate side-chains 284 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 1966 ARG Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2349 LYS Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4422 LYS Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4547 THR Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 112 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 106 optimal weight: 0.0570 chunk 220 optimal weight: 0.5980 chunk 131 optimal weight: 0.0270 chunk 161 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1559 HIS ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3526 GLN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112188 restraints weight = 45057.067| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.51 r_work: 0.3536 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23578 Z= 0.114 Angle : 0.547 8.060 31985 Z= 0.276 Chirality : 0.039 0.164 3600 Planarity : 0.004 0.055 4087 Dihedral : 6.391 109.677 3193 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Rotamer: Outliers : 2.17 % Allowed : 14.80 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2841 helix: 2.05 (0.13), residues: 1583 sheet: -1.06 (0.35), residues: 226 loop : -0.57 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2500 HIS 0.004 0.001 HIS A2637 PHE 0.024 0.001 PHE A4122 TYR 0.024 0.001 TYR A3812 ARG 0.006 0.000 ARG A3728 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 1309) hydrogen bonds : angle 4.11770 ( 3825) covalent geometry : bond 0.00248 (23578) covalent geometry : angle 0.54714 (31985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7041 (mmt-90) cc_final: 0.6633 (mmt-90) REVERT: A 1574 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6641 (tp30) REVERT: A 1709 MET cc_start: 0.8055 (tmm) cc_final: 0.7739 (ttt) REVERT: A 1769 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6803 (mmt) REVERT: A 1825 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5840 (tt) REVERT: A 1966 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7477 (ttp80) REVERT: A 1969 SER cc_start: 0.8628 (t) cc_final: 0.8098 (m) REVERT: A 2292 ARG cc_start: 0.7002 (mpp80) cc_final: 0.6738 (mpp80) REVERT: A 2603 MET cc_start: 0.6802 (mmp) cc_final: 0.6487 (mmm) REVERT: A 2654 GLN cc_start: 0.8587 (tp40) cc_final: 0.8317 (tp-100) REVERT: A 2752 ASN cc_start: 0.8760 (m-40) cc_final: 0.8465 (m110) REVERT: A 2755 MET cc_start: 0.6869 (ttp) cc_final: 0.6351 (ttp) REVERT: A 2799 MET cc_start: 0.7526 (mtp) cc_final: 0.7319 (mtp) REVERT: A 2839 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7384 (tt0) REVERT: A 2845 TRP cc_start: 0.7784 (t-100) cc_final: 0.7444 (t-100) REVERT: A 2930 GLN cc_start: 0.6451 (mm110) cc_final: 0.5824 (tt0) REVERT: A 3053 TRP cc_start: 0.7281 (t60) cc_final: 0.6817 (t-100) REVERT: A 3178 ASP cc_start: 0.7190 (t0) cc_final: 0.6792 (t0) REVERT: A 3497 LYS cc_start: 0.8350 (mmpt) cc_final: 0.7915 (mtpt) REVERT: A 3540 ASN cc_start: 0.8984 (t0) cc_final: 0.8539 (t0) REVERT: A 3718 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7324 (mtmm) REVERT: A 3741 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6035 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6384 (mmt-90) cc_final: 0.5569 (mmp-170) REVERT: A 3751 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6396 (mm110) REVERT: A 3885 MET cc_start: 0.8466 (mmm) cc_final: 0.8207 (mmm) REVERT: A 4021 MET cc_start: 0.7836 (mmp) cc_final: 0.7447 (mmm) REVERT: A 4107 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6744 (mmm) REVERT: A 4111 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8545 (mmtt) REVERT: A 4169 ILE cc_start: 0.8454 (tt) cc_final: 0.8198 (tt) REVERT: A 4192 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 4233 ILE cc_start: 0.7764 (tt) cc_final: 0.7500 (pt) outliers start: 55 outliers final: 31 residues processed: 309 average time/residue: 0.3761 time to fit residues: 182.5017 Evaluate side-chains 285 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1936 PHE Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 1966 ARG Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 259 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1541 GLN A1559 HIS A1643 ASN A2860 ASN ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110044 restraints weight = 44917.016| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.50 r_work: 0.3502 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23578 Z= 0.154 Angle : 0.577 10.493 31985 Z= 0.290 Chirality : 0.040 0.161 3600 Planarity : 0.004 0.056 4087 Dihedral : 6.315 109.785 3193 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.20 % Allowed : 16.02 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2841 helix: 1.98 (0.13), residues: 1585 sheet: -1.05 (0.35), residues: 228 loop : -0.62 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2500 HIS 0.004 0.001 HIS A2637 PHE 0.019 0.001 PHE A3813 TYR 0.025 0.001 TYR A3812 ARG 0.007 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1309) hydrogen bonds : angle 4.17934 ( 3825) covalent geometry : bond 0.00361 (23578) covalent geometry : angle 0.57679 (31985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1574 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6692 (tp30) REVERT: A 1966 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7472 (ttp80) REVERT: A 1969 SER cc_start: 0.8718 (t) cc_final: 0.8211 (m) REVERT: A 2603 MET cc_start: 0.6806 (mmp) cc_final: 0.6480 (mmm) REVERT: A 2752 ASN cc_start: 0.8776 (m-40) cc_final: 0.8482 (m110) REVERT: A 2755 MET cc_start: 0.6968 (ttp) cc_final: 0.6386 (ttp) REVERT: A 2799 MET cc_start: 0.7791 (mtp) cc_final: 0.7588 (mtp) REVERT: A 2845 TRP cc_start: 0.7771 (t-100) cc_final: 0.7417 (t-100) REVERT: A 2930 GLN cc_start: 0.6453 (mm110) cc_final: 0.5821 (tt0) REVERT: A 3053 TRP cc_start: 0.7345 (t60) cc_final: 0.6822 (t-100) REVERT: A 3178 ASP cc_start: 0.7245 (t0) cc_final: 0.6858 (t0) REVERT: A 3497 LYS cc_start: 0.8411 (mmpt) cc_final: 0.7900 (mtpt) REVERT: A 3540 ASN cc_start: 0.9009 (t0) cc_final: 0.8571 (t0) REVERT: A 3659 ARG cc_start: 0.5551 (mmm160) cc_final: 0.4243 (tpt-90) REVERT: A 3718 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7375 (mtmm) REVERT: A 3741 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5875 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6389 (mmt-90) cc_final: 0.5550 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6250 (mm110) REVERT: A 3816 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: A 3885 MET cc_start: 0.8541 (mmm) cc_final: 0.8288 (mmm) REVERT: A 4021 MET cc_start: 0.8033 (mmp) cc_final: 0.7701 (mmp) REVERT: A 4107 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7039 (mmm) REVERT: A 4111 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8553 (mmtt) REVERT: A 4169 ILE cc_start: 0.8479 (tt) cc_final: 0.8253 (tt) REVERT: A 4192 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 4233 ILE cc_start: 0.7772 (tt) cc_final: 0.7429 (pt) outliers start: 56 outliers final: 39 residues processed: 299 average time/residue: 0.4031 time to fit residues: 188.5060 Evaluate side-chains 285 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 1966 ARG Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2349 LYS Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 GLU Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 81 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 281 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A3563 GLN A3646 ASN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111655 restraints weight = 44997.663| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.67 r_work: 0.3520 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23578 Z= 0.115 Angle : 0.548 11.241 31985 Z= 0.276 Chirality : 0.039 0.151 3600 Planarity : 0.004 0.055 4087 Dihedral : 6.093 105.291 3193 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 1.85 % Allowed : 16.81 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2841 helix: 2.10 (0.13), residues: 1588 sheet: -0.87 (0.34), residues: 241 loop : -0.62 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2234 HIS 0.004 0.001 HIS A2637 PHE 0.018 0.001 PHE A3813 TYR 0.041 0.001 TYR A3812 ARG 0.010 0.000 ARG A1542 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 1309) hydrogen bonds : angle 4.04596 ( 3825) covalent geometry : bond 0.00253 (23578) covalent geometry : angle 0.54797 (31985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7094 (mmt-90) cc_final: 0.6893 (mmt-90) REVERT: A 1574 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6740 (tp30) REVERT: A 1966 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: A 1969 SER cc_start: 0.8677 (t) cc_final: 0.8170 (m) REVERT: A 2292 ARG cc_start: 0.7279 (mpp80) cc_final: 0.6986 (mpp80) REVERT: A 2353 LEU cc_start: 0.8705 (tp) cc_final: 0.8501 (tt) REVERT: A 2545 TRP cc_start: 0.6312 (m100) cc_final: 0.5963 (m100) REVERT: A 2603 MET cc_start: 0.6827 (mmp) cc_final: 0.6507 (mmm) REVERT: A 2752 ASN cc_start: 0.8745 (m-40) cc_final: 0.8435 (m110) REVERT: A 2755 MET cc_start: 0.6848 (ttp) cc_final: 0.6318 (ttp) REVERT: A 2799 MET cc_start: 0.7697 (mtp) cc_final: 0.7492 (mtp) REVERT: A 2839 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7421 (tt0) REVERT: A 2845 TRP cc_start: 0.7735 (t-100) cc_final: 0.7460 (t-100) REVERT: A 2930 GLN cc_start: 0.6486 (mm110) cc_final: 0.6159 (tt0) REVERT: A 3053 TRP cc_start: 0.7320 (t60) cc_final: 0.6807 (t-100) REVERT: A 3178 ASP cc_start: 0.7226 (t0) cc_final: 0.6874 (t0) REVERT: A 3497 LYS cc_start: 0.8405 (mmpt) cc_final: 0.7939 (mtpt) REVERT: A 3540 ASN cc_start: 0.9053 (t0) cc_final: 0.8587 (t0) REVERT: A 3718 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7355 (mtmm) REVERT: A 3741 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5785 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6420 (mmt-90) cc_final: 0.5606 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6326 (mm110) REVERT: A 3794 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7519 (t) REVERT: A 3816 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: A 3885 MET cc_start: 0.8495 (mmm) cc_final: 0.8255 (mmm) REVERT: A 4021 MET cc_start: 0.7937 (mmp) cc_final: 0.7138 (mmp) REVERT: A 4107 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (mmm) REVERT: A 4111 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8533 (mmtt) REVERT: A 4169 ILE cc_start: 0.8406 (tt) cc_final: 0.8169 (tt) REVERT: A 4192 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 4233 ILE cc_start: 0.7766 (tt) cc_final: 0.7488 (pt) outliers start: 47 outliers final: 34 residues processed: 295 average time/residue: 0.4133 time to fit residues: 192.0370 Evaluate side-chains 286 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 1966 ARG Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2349 LYS Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 48 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 272 optimal weight: 7.9990 chunk 60 optimal weight: 0.0370 chunk 273 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.110876 restraints weight = 44689.139| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.65 r_work: 0.3510 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23578 Z= 0.131 Angle : 0.562 11.469 31985 Z= 0.284 Chirality : 0.039 0.162 3600 Planarity : 0.004 0.050 4087 Dihedral : 6.060 103.256 3193 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 2.24 % Allowed : 16.81 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2841 helix: 2.09 (0.13), residues: 1585 sheet: -0.87 (0.34), residues: 242 loop : -0.60 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2500 HIS 0.003 0.001 HIS A2637 PHE 0.018 0.001 PHE A3813 TYR 0.030 0.001 TYR A3812 ARG 0.008 0.000 ARG A1542 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 1309) hydrogen bonds : angle 4.05636 ( 3825) covalent geometry : bond 0.00301 (23578) covalent geometry : angle 0.56211 (31985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1574 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6719 (tp30) REVERT: A 1584 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7976 (mtmm) REVERT: A 1969 SER cc_start: 0.8717 (t) cc_final: 0.8248 (m) REVERT: A 2545 TRP cc_start: 0.6296 (m100) cc_final: 0.5933 (m100) REVERT: A 2603 MET cc_start: 0.6812 (mmp) cc_final: 0.6483 (mmm) REVERT: A 2752 ASN cc_start: 0.8747 (m-40) cc_final: 0.8453 (m110) REVERT: A 2755 MET cc_start: 0.6996 (ttp) cc_final: 0.6422 (ttp) REVERT: A 2799 MET cc_start: 0.7692 (mtp) cc_final: 0.7490 (mtp) REVERT: A 2839 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7339 (tt0) REVERT: A 2845 TRP cc_start: 0.7703 (t-100) cc_final: 0.7459 (t-100) REVERT: A 2930 GLN cc_start: 0.6499 (mm110) cc_final: 0.6160 (tt0) REVERT: A 3053 TRP cc_start: 0.7365 (t60) cc_final: 0.6836 (t-100) REVERT: A 3178 ASP cc_start: 0.7275 (t0) cc_final: 0.6913 (t0) REVERT: A 3497 LYS cc_start: 0.8420 (mmpt) cc_final: 0.7947 (mtpt) REVERT: A 3540 ASN cc_start: 0.9024 (t0) cc_final: 0.8584 (t0) REVERT: A 3718 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7483 (mtmm) REVERT: A 3741 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5880 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6421 (mmt-90) cc_final: 0.5586 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6272 (mm110) REVERT: A 3772 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6511 (p0) REVERT: A 3816 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: A 3885 MET cc_start: 0.8486 (mmm) cc_final: 0.8258 (mmm) REVERT: A 4021 MET cc_start: 0.8006 (mmp) cc_final: 0.7722 (mmp) REVERT: A 4107 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7121 (mmm) REVERT: A 4111 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8568 (mmtt) REVERT: A 4169 ILE cc_start: 0.8390 (tt) cc_final: 0.8176 (tt) REVERT: A 4192 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 4233 ILE cc_start: 0.7770 (tt) cc_final: 0.7473 (pt) outliers start: 57 outliers final: 41 residues processed: 299 average time/residue: 0.3861 time to fit residues: 181.1799 Evaluate side-chains 288 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 GLU Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 224 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 121 optimal weight: 0.0870 chunk 274 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A1810 HIS ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111629 restraints weight = 44901.951| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.65 r_work: 0.3524 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23578 Z= 0.120 Angle : 0.560 10.341 31985 Z= 0.282 Chirality : 0.039 0.193 3600 Planarity : 0.004 0.050 4087 Dihedral : 5.986 100.048 3193 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 17.36 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2841 helix: 2.13 (0.13), residues: 1585 sheet: -0.96 (0.34), residues: 250 loop : -0.58 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2500 HIS 0.004 0.001 HIS A1810 PHE 0.017 0.001 PHE A3813 TYR 0.025 0.001 TYR A3812 ARG 0.007 0.000 ARG A3728 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 1309) hydrogen bonds : angle 4.00785 ( 3825) covalent geometry : bond 0.00271 (23578) covalent geometry : angle 0.56004 (31985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7190 (mmt-90) cc_final: 0.6858 (mmp80) REVERT: A 1574 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6747 (tp30) REVERT: A 1584 LYS cc_start: 0.8213 (mtmm) cc_final: 0.8004 (mtmm) REVERT: A 1969 SER cc_start: 0.8669 (t) cc_final: 0.8159 (m) REVERT: A 2367 ASP cc_start: 0.7697 (t0) cc_final: 0.7475 (t0) REVERT: A 2545 TRP cc_start: 0.6278 (m100) cc_final: 0.5916 (m100) REVERT: A 2603 MET cc_start: 0.6784 (mmp) cc_final: 0.6459 (mmm) REVERT: A 2752 ASN cc_start: 0.8731 (m-40) cc_final: 0.8463 (m110) REVERT: A 2755 MET cc_start: 0.6936 (ttp) cc_final: 0.6361 (ttp) REVERT: A 2839 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7344 (tt0) REVERT: A 2845 TRP cc_start: 0.7707 (t-100) cc_final: 0.7459 (t-100) REVERT: A 3053 TRP cc_start: 0.7370 (t60) cc_final: 0.6841 (t-100) REVERT: A 3178 ASP cc_start: 0.7246 (t0) cc_final: 0.6904 (t0) REVERT: A 3497 LYS cc_start: 0.8372 (mmpt) cc_final: 0.7945 (mtpt) REVERT: A 3530 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7375 (m) REVERT: A 3540 ASN cc_start: 0.9049 (t0) cc_final: 0.8577 (t0) REVERT: A 3718 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7482 (mtmm) REVERT: A 3741 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5982 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6461 (mmt-90) cc_final: 0.5626 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6364 (mm110) REVERT: A 3772 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6528 (p0) REVERT: A 3885 MET cc_start: 0.8457 (mmm) cc_final: 0.8226 (mmm) REVERT: A 4021 MET cc_start: 0.7965 (mmp) cc_final: 0.7650 (mmp) REVERT: A 4107 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7063 (mmm) REVERT: A 4111 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8525 (mmtt) REVERT: A 4169 ILE cc_start: 0.8360 (tt) cc_final: 0.8144 (tt) REVERT: A 4192 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 4233 ILE cc_start: 0.7714 (tt) cc_final: 0.7443 (pt) outliers start: 54 outliers final: 41 residues processed: 302 average time/residue: 0.3955 time to fit residues: 188.6093 Evaluate side-chains 289 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3530 THR Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4107 MET Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 217 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113142 restraints weight = 44336.371| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.34 r_work: 0.3543 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23578 Z= 0.142 Angle : 0.588 11.189 31985 Z= 0.295 Chirality : 0.040 0.282 3600 Planarity : 0.004 0.049 4087 Dihedral : 6.027 98.985 3193 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.09 % Allowed : 17.72 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2841 helix: 2.10 (0.13), residues: 1582 sheet: -0.87 (0.34), residues: 242 loop : -0.60 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2500 HIS 0.004 0.001 HIS A1810 PHE 0.018 0.001 PHE A3813 TYR 0.032 0.001 TYR A3812 ARG 0.007 0.000 ARG A3728 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1309) hydrogen bonds : angle 4.06200 ( 3825) covalent geometry : bond 0.00330 (23578) covalent geometry : angle 0.58752 (31985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7397 (mmt-90) cc_final: 0.6929 (mmt-90) REVERT: A 1574 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6733 (tp30) REVERT: A 1969 SER cc_start: 0.8723 (t) cc_final: 0.8307 (m) REVERT: A 2603 MET cc_start: 0.6742 (mmp) cc_final: 0.6433 (mmm) REVERT: A 2755 MET cc_start: 0.7030 (ttp) cc_final: 0.6574 (ttp) REVERT: A 2839 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7463 (tt0) REVERT: A 3053 TRP cc_start: 0.7568 (t60) cc_final: 0.6970 (t-100) REVERT: A 3178 ASP cc_start: 0.7308 (t0) cc_final: 0.7044 (t0) REVERT: A 3497 LYS cc_start: 0.8461 (mmpt) cc_final: 0.8110 (mtpt) REVERT: A 3530 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7465 (m) REVERT: A 3540 ASN cc_start: 0.8795 (t0) cc_final: 0.8533 (t0) REVERT: A 3739 GLN cc_start: 0.7316 (pm20) cc_final: 0.6957 (pm20) REVERT: A 3741 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5940 (pmt-80) REVERT: A 3743 ARG cc_start: 0.6654 (mmt-90) cc_final: 0.5779 (mmp-170) REVERT: A 3751 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6166 (mm110) REVERT: A 3772 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6594 (p0) REVERT: A 3794 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7910 (t) REVERT: A 3885 MET cc_start: 0.8350 (mmm) cc_final: 0.8070 (mmm) REVERT: A 4021 MET cc_start: 0.8048 (mmp) cc_final: 0.7669 (mmp) REVERT: A 4111 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8624 (mmtt) REVERT: A 4169 ILE cc_start: 0.8639 (tt) cc_final: 0.8422 (tt) REVERT: A 4233 ILE cc_start: 0.7779 (tt) cc_final: 0.7568 (pt) outliers start: 53 outliers final: 41 residues processed: 286 average time/residue: 0.3809 time to fit residues: 169.9366 Evaluate side-chains 285 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3530 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3751 GLN Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4545 VAL Chi-restraints excluded: chain A residue 4622 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 237 optimal weight: 0.0970 chunk 149 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 275 optimal weight: 0.0270 chunk 234 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 284 optimal weight: 0.0670 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.140611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116957 restraints weight = 43907.064| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.45 r_work: 0.3588 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23578 Z= 0.112 Angle : 0.569 10.774 31985 Z= 0.286 Chirality : 0.039 0.241 3600 Planarity : 0.004 0.052 4087 Dihedral : 5.829 93.292 3193 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 1.85 % Allowed : 18.15 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2841 helix: 2.19 (0.13), residues: 1578 sheet: -0.96 (0.33), residues: 252 loop : -0.57 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP A2845 HIS 0.002 0.000 HIS A1559 PHE 0.019 0.001 PHE A3629 TYR 0.035 0.001 TYR A3812 ARG 0.008 0.000 ARG A3728 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1309) hydrogen bonds : angle 3.96971 ( 3825) covalent geometry : bond 0.00242 (23578) covalent geometry : angle 0.56897 (31985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11547.60 seconds wall clock time: 203 minutes 4.95 seconds (12184.95 seconds total)