Starting phenix.real_space_refine on Fri May 23 00:45:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmp_44706/05_2025/9bmp_44706.cif" } resolution = 3.5 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= -0.000 sd= 0.043 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 14703 2.51 5 N 3988 2.21 5 O 4294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23110 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2858, 22994 Classifications: {'peptide': 2858} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 129, 'TRANS': 2728} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ANP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.07, per 1000 atoms: 0.57 Number of scatterers: 23110 At special positions: 0 Unit cell: (149.73, 151.032, 124.992, 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 4294 8.00 N 3988 7.00 C 14703 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: 5.86 Conformation dependent library (CDL) restraints added in 3.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 19 sheets defined 61.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 1460 through 1472 Processing helix chain 'A' and resid 1489 through 1509 Processing helix chain 'A' and resid 1510 through 1515 removed outlier: 3.959A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.764A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1594 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1631 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.500A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.755A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.501A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.543A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1824 Processing helix chain 'A' and resid 1835 through 1840 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: 3.686A pdb=" N MET A1941 " --> pdb=" O ASP A1937 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.521A pdb=" N ARG A1962 " --> pdb=" O GLU A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1985 Processing helix chain 'A' and resid 2045 through 2057 removed outlier: 3.586A pdb=" N GLN A2051 " --> pdb=" O GLN A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2079 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 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: 4.205A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.745A pdb=" N GLU A2180 " --> pdb=" O THR A2176 " (cutoff:3.500A) removed outlier: 4.304A 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 2230 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2315 through 2320 removed outlier: 3.500A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.524A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 4.065A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 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: 3.571A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.824A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.722A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.978A 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 2756 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 3.834A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2757 through 2764' Processing helix chain 'A' and resid 2765 through 2783 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.973A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (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 2885 through 2903 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.562A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2995 through 2999 Processing helix chain 'A' and resid 3001 through 3005 Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.506A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 removed outlier: 3.672A 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 3062 Processing helix chain 'A' and resid 3084 through 3089 removed outlier: 3.902A pdb=" N CYS A3089 " --> pdb=" O LEU A3085 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.590A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3502 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.791A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 removed outlier: 3.630A pdb=" N ARG A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.557A pdb=" N TYR A3604 " --> pdb=" O ILE A3600 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3629 removed outlier: 3.767A pdb=" N PHE A3629 " --> pdb=" O SER A3625 " (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: 3.694A 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 3734 Processing helix chain 'A' and resid 3736 through 3757 Processing helix chain 'A' and resid 3762 through 3818 removed outlier: 3.660A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP A3788 " --> pdb=" O VAL A3784 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A3789 " --> pdb=" O GLU A3785 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.537A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.627A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 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 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.140A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.656A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 4.013A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.988A pdb=" N PHE A4077 " --> pdb=" O SER A4073 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.630A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.767A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 3.897A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) 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 removed outlier: 3.581A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.592A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.636A 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 4325 through 4346 removed outlier: 4.361A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.736A pdb=" N GLU A4439 " --> pdb=" O VAL A4435 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 3.871A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4500 through 4506' 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 4638 removed outlier: 3.535A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.142A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 3.686A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.649A 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: 6.435A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.248A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 6.607A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A2345 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A2222 " --> pdb=" O VAL A2345 " (cutoff:3.500A) 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 2324 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: 6.324A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASP A2664 " --> pdb=" O VAL A2618 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A2620 " --> pdb=" O ASP A2664 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.143A 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: 3.554A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 5.855A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A3066 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.399A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3661 through 3664 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.154A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 3.884A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A4287 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS A4292 " --> pdb=" O LYS A4287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.679A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.840A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3813 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: 12.88 Time building geometry restraints manager: 6.88 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: 7592 1.34 - 1.46: 5235 1.46 - 1.58: 10580 1.58 - 1.70: 12 1.70 - 1.82: 192 Bond restraints: 23611 Sorted by residual: bond pdb=" O3A ANP A4703 " pdb=" PB ANP A4703 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O5' ANP A4703 " pdb=" PA ANP A4703 " ideal model delta sigma weight residual 1.655 1.583 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O3G ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C MET A3126 " pdb=" N PRO A3127 " ideal model delta sigma weight residual 1.335 1.357 -0.022 8.70e-03 1.32e+04 6.12e+00 ... (remaining 23606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 31859 3.59 - 7.17: 146 7.17 - 10.76: 18 10.76 - 14.34: 5 14.34 - 17.93: 1 Bond angle restraints: 32029 Sorted by residual: angle pdb=" PB ANP A4703 " pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 126.95 109.02 17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" N LEU A2387 " pdb=" CA LEU A2387 " pdb=" C LEU A2387 " ideal model delta sigma weight residual 113.21 107.18 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" CB MET A4419 " pdb=" CG MET A4419 " pdb=" SD MET A4419 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" N GLU A2864 " pdb=" CA GLU A2864 " pdb=" C GLU A2864 " ideal model delta sigma weight residual 114.31 109.25 5.06 1.29e+00 6.01e-01 1.54e+01 angle pdb=" C SER A2878 " pdb=" CA SER A2878 " pdb=" CB SER A2878 " ideal model delta sigma weight residual 115.89 110.96 4.93 1.32e+00 5.74e-01 1.39e+01 ... (remaining 32024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 12398 17.86 - 35.71: 1492 35.71 - 53.57: 311 53.57 - 71.43: 85 71.43 - 89.29: 37 Dihedral angle restraints: 14323 sinusoidal: 5952 harmonic: 8371 Sorted by residual: dihedral pdb=" CA THR A4127 " pdb=" C THR A4127 " pdb=" N MET A4128 " pdb=" CA MET A4128 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 4.88 -64.88 1 2.00e+01 2.50e-03 1.38e+01 dihedral pdb=" CA ILE A2521 " pdb=" C ILE A2521 " pdb=" N THR A2522 " pdb=" CA THR A2522 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3203 0.066 - 0.132: 375 0.132 - 0.198: 21 0.198 - 0.263: 1 0.263 - 0.329: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" CB ILE A2936 " pdb=" CA ILE A2936 " pdb=" CG1 ILE A2936 " pdb=" CG2 ILE A2936 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU A1547 " pdb=" CB LEU A1547 " pdb=" CD1 LEU A1547 " pdb=" CD2 LEU A1547 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ANP A4703 " pdb=" C2' ANP A4703 " pdb=" C4' ANP A4703 " pdb=" O3' ANP A4703 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3600 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A3123 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A3126 " -0.054 5.00e-02 4.00e+02 8.31e-02 1.11e+01 pdb=" N PRO A3127 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A3127 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3127 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A3082 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A3083 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A3083 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A3083 " -0.041 5.00e-02 4.00e+02 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 352 2.67 - 3.23: 22977 3.23 - 3.78: 37497 3.78 - 4.34: 48402 4.34 - 4.90: 79735 Nonbonded interactions: 188963 Sorted by model distance: nonbonded pdb=" O GLU A1548 " pdb=" OG1 THR A1552 " model vdw 2.108 3.040 nonbonded pdb=" O LEU A1561 " pdb=" OG1 THR A1565 " model vdw 2.144 3.040 nonbonded pdb=" OG SER A2231 " pdb=" O1B ATP A4702 " model vdw 2.185 3.040 nonbonded pdb=" O LEU A4272 " pdb=" OG SER A4277 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A3812 " pdb=" OE2 GLU A3816 " model vdw 2.271 3.040 ... (remaining 188958 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 group one per residue 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: 1.050 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 57.750 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.144 23611 Z= 0.160 Angle : 0.684 17.929 32029 Z= 0.346 Chirality : 0.042 0.329 3603 Planarity : 0.005 0.106 4094 Dihedral : 16.619 89.286 8883 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 0.39 % Allowed : 16.12 % Favored : 83.49 % 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: 1.15 (0.16), residues: 2844 helix: 1.67 (0.13), residues: 1571 sheet: -0.80 (0.33), residues: 238 loop : -0.17 (0.21), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1523 HIS 0.011 0.001 HIS A2932 PHE 0.032 0.001 PHE A4482 TYR 0.021 0.001 TYR A3183 ARG 0.007 0.000 ARG A3561 Details of bonding type rmsd hydrogen bonds : bond 0.12538 ( 1303) hydrogen bonds : angle 5.57194 ( 3813) covalent geometry : bond 0.00332 (23611) covalent geometry : angle 0.68388 (32029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 282 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1463 LEU cc_start: 0.7297 (mt) cc_final: 0.6913 (pp) REVERT: A 1967 MET cc_start: 0.7820 (tpt) cc_final: 0.7602 (tpt) REVERT: A 2975 ASP cc_start: 0.8763 (p0) cc_final: 0.8299 (m-30) REVERT: A 2995 ASP cc_start: 0.7536 (t0) cc_final: 0.7258 (t70) outliers start: 10 outliers final: 3 residues processed: 287 average time/residue: 0.3239 time to fit residues: 150.0702 Evaluate side-chains 266 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0270 chunk 216 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A1748 GLN A2491 GLN A2791 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A3200 HIS A3709 GLN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.144171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108487 restraints weight = 45579.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112256 restraints weight = 22088.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114772 restraints weight = 14535.185| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23611 Z= 0.162 Angle : 0.591 8.369 32029 Z= 0.294 Chirality : 0.042 0.190 3603 Planarity : 0.005 0.058 4094 Dihedral : 6.746 102.738 3199 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 15.49 % Favored : 82.31 % 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: 1.61 (0.16), residues: 2844 helix: 2.12 (0.13), residues: 1591 sheet: -0.75 (0.33), residues: 237 loop : -0.09 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1523 HIS 0.008 0.001 HIS A2932 PHE 0.019 0.001 PHE A3066 TYR 0.033 0.001 TYR A2901 ARG 0.010 0.001 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 1303) hydrogen bonds : angle 4.14475 ( 3813) covalent geometry : bond 0.00373 (23611) covalent geometry : angle 0.59082 (32029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 2.461 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 1463 LEU cc_start: 0.7453 (mt) cc_final: 0.6980 (pp) REVERT: A 1937 ASP cc_start: 0.7500 (p0) cc_final: 0.7194 (p0) REVERT: A 1941 MET cc_start: 0.8098 (tpp) cc_final: 0.7727 (tpp) REVERT: A 1962 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7951 (ptm-80) REVERT: A 2037 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8425 (ttm-80) REVERT: A 2959 TYR cc_start: 0.7019 (t80) cc_final: 0.6641 (t80) REVERT: A 2975 ASP cc_start: 0.8640 (p0) cc_final: 0.8406 (m-30) REVERT: A 3126 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5929 (pmm) REVERT: A 3524 MET cc_start: 0.8952 (tpp) cc_final: 0.8579 (tpp) REVERT: A 3714 ASN cc_start: 0.8795 (m-40) cc_final: 0.8594 (m-40) REVERT: A 3730 ASP cc_start: 0.7807 (m-30) cc_final: 0.7597 (t0) outliers start: 56 outliers final: 24 residues processed: 317 average time/residue: 0.3436 time to fit residues: 173.5100 Evaluate side-chains 276 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 199 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** A1736 ASN A2827 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 HIS A3181 ASN A3534 HIS A3538 GLN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104190 restraints weight = 46160.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107896 restraints weight = 22568.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110289 restraints weight = 14882.080| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23611 Z= 0.231 Angle : 0.630 9.482 32029 Z= 0.313 Chirality : 0.043 0.181 3603 Planarity : 0.004 0.056 4094 Dihedral : 6.317 99.990 3196 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.83 % Allowed : 16.47 % Favored : 80.70 % 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: 1.52 (0.16), residues: 2844 helix: 2.06 (0.13), residues: 1597 sheet: -0.73 (0.32), residues: 251 loop : -0.20 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1523 HIS 0.029 0.002 HIS A3155 PHE 0.047 0.002 PHE A2635 TYR 0.030 0.002 TYR A2901 ARG 0.006 0.000 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1303) hydrogen bonds : angle 4.15973 ( 3813) covalent geometry : bond 0.00544 (23611) covalent geometry : angle 0.62992 (32029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 266 time to evaluate : 2.578 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 1463 LEU cc_start: 0.7686 (mt) cc_final: 0.7231 (pp) REVERT: A 1651 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: A 1941 MET cc_start: 0.8174 (tpp) cc_final: 0.7866 (tpp) REVERT: A 1962 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.8083 (ptm-80) REVERT: A 2779 MET cc_start: 0.8554 (mpp) cc_final: 0.8169 (mpp) REVERT: A 3126 MET cc_start: 0.6158 (ppp) cc_final: 0.5956 (pmm) REVERT: A 3524 MET cc_start: 0.8976 (tpp) cc_final: 0.8751 (tpp) REVERT: A 3712 CYS cc_start: 0.8245 (m) cc_final: 0.7858 (m) REVERT: A 3839 VAL cc_start: 0.9189 (p) cc_final: 0.8934 (p) REVERT: A 4238 ILE cc_start: 0.8647 (mm) cc_final: 0.8425 (mm) outliers start: 72 outliers final: 48 residues processed: 314 average time/residue: 0.3404 time to fit residues: 172.7343 Evaluate side-chains 292 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3128 VAL Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3579 MET Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4056 GLU Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4397 HIS Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4572 ASN Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 235 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN A3843 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105006 restraints weight = 46259.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108721 restraints weight = 22517.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111166 restraints weight = 14863.908| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23611 Z= 0.170 Angle : 0.577 9.801 32029 Z= 0.287 Chirality : 0.041 0.180 3603 Planarity : 0.004 0.061 4094 Dihedral : 6.074 103.095 3196 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.52 % Allowed : 18.20 % Favored : 79.28 % 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: 1.57 (0.16), residues: 2844 helix: 2.09 (0.13), residues: 1605 sheet: -0.72 (0.33), residues: 226 loop : -0.20 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2845 HIS 0.007 0.001 HIS A2932 PHE 0.050 0.002 PHE A2635 TYR 0.036 0.001 TYR A2901 ARG 0.005 0.000 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1303) hydrogen bonds : angle 4.01430 ( 3813) covalent geometry : bond 0.00393 (23611) covalent geometry : angle 0.57737 (32029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 2.462 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: A 1463 LEU cc_start: 0.7853 (mt) cc_final: 0.7539 (pp) REVERT: A 1651 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: A 1941 MET cc_start: 0.8167 (tpp) cc_final: 0.7871 (tpp) REVERT: A 3126 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5977 (pmm) REVERT: A 3169 MET cc_start: 0.7187 (mmm) cc_final: 0.6936 (mmm) REVERT: A 3199 MET cc_start: 0.6482 (tmm) cc_final: 0.6143 (tmm) REVERT: A 3524 MET cc_start: 0.9032 (tpp) cc_final: 0.8804 (tpp) REVERT: A 3712 CYS cc_start: 0.8244 (m) cc_final: 0.7867 (m) REVERT: A 3791 MET cc_start: 0.8233 (mtp) cc_final: 0.8023 (mtp) REVERT: A 4117 GLN cc_start: 0.6583 (mm-40) cc_final: 0.6222 (mp10) REVERT: A 4238 ILE cc_start: 0.8662 (mm) cc_final: 0.8451 (mm) REVERT: A 4459 ILE cc_start: 0.9169 (mm) cc_final: 0.8934 (mp) outliers start: 64 outliers final: 44 residues processed: 299 average time/residue: 0.3360 time to fit residues: 162.0488 Evaluate side-chains 282 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4056 GLU Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 268 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 193 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 240 optimal weight: 0.0370 chunk 135 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- 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** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105067 restraints weight = 45790.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108819 restraints weight = 22219.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111238 restraints weight = 14591.849| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23611 Z= 0.156 Angle : 0.569 12.507 32029 Z= 0.283 Chirality : 0.041 0.177 3603 Planarity : 0.004 0.062 4094 Dihedral : 5.894 105.291 3196 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.11 % Allowed : 18.08 % Favored : 78.81 % 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: 1.60 (0.16), residues: 2844 helix: 2.09 (0.13), residues: 1606 sheet: -0.64 (0.34), residues: 224 loop : -0.16 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A2845 HIS 0.007 0.001 HIS A2932 PHE 0.054 0.002 PHE A2635 TYR 0.038 0.002 TYR A2901 ARG 0.009 0.000 ARG A2783 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1303) hydrogen bonds : angle 3.95035 ( 3813) covalent geometry : bond 0.00362 (23611) covalent geometry : angle 0.56944 (32029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 2.393 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 1463 LEU cc_start: 0.7959 (mt) cc_final: 0.7597 (pp) REVERT: A 1651 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: A 1941 MET cc_start: 0.8141 (tpp) cc_final: 0.7833 (tpp) REVERT: A 2105 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7181 (mtm110) REVERT: A 4459 ILE cc_start: 0.9175 (mm) cc_final: 0.8943 (mp) REVERT: A 4623 ASP cc_start: 0.7856 (m-30) cc_final: 0.7115 (p0) outliers start: 79 outliers final: 49 residues processed: 317 average time/residue: 0.3336 time to fit residues: 170.6267 Evaluate side-chains 288 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3150 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4056 GLU Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4397 HIS Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 118 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 127 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 276 optimal weight: 0.0070 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN A4381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107813 restraints weight = 45563.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111634 restraints weight = 21970.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.114098 restraints weight = 14317.748| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23611 Z= 0.112 Angle : 0.546 9.024 32029 Z= 0.270 Chirality : 0.040 0.186 3603 Planarity : 0.004 0.054 4094 Dihedral : 5.759 107.060 3196 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 2.32 % Allowed : 19.34 % Favored : 78.34 % 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: 1.82 (0.16), residues: 2844 helix: 2.28 (0.13), residues: 1592 sheet: -0.47 (0.34), residues: 224 loop : -0.07 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1523 HIS 0.007 0.001 HIS A2932 PHE 0.053 0.001 PHE A2635 TYR 0.038 0.001 TYR A2901 ARG 0.003 0.000 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1303) hydrogen bonds : angle 3.85452 ( 3813) covalent geometry : bond 0.00246 (23611) covalent geometry : angle 0.54626 (32029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 2.459 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: A 1463 LEU cc_start: 0.8006 (mt) cc_final: 0.7587 (pp) REVERT: A 1607 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5513 (tt) REVERT: A 1651 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: A 1941 MET cc_start: 0.8097 (tpp) cc_final: 0.7822 (tpp) REVERT: A 2105 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7139 (mtm110) REVERT: A 2799 MET cc_start: 0.8368 (mmm) cc_final: 0.8161 (mmm) REVERT: A 2930 GLN cc_start: 0.5985 (mm-40) cc_final: 0.5193 (tt0) REVERT: A 3527 ASN cc_start: 0.8246 (t0) cc_final: 0.8016 (t0) REVERT: A 4459 ILE cc_start: 0.9153 (mm) cc_final: 0.8891 (mp) REVERT: A 4617 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7339 (p0) REVERT: A 4623 ASP cc_start: 0.7745 (m-30) cc_final: 0.7097 (p0) outliers start: 59 outliers final: 36 residues processed: 318 average time/residue: 0.3212 time to fit residues: 166.3069 Evaluate side-chains 290 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2520 ARG Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 4056 GLU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 207 optimal weight: 0.7980 chunk 200 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2791 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3032 GLN A3181 ASN A3540 ASN A3709 GLN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4530 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.143049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107640 restraints weight = 45814.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.111450 restraints weight = 22060.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113882 restraints weight = 14375.947| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23611 Z= 0.120 Angle : 0.554 9.921 32029 Z= 0.273 Chirality : 0.040 0.176 3603 Planarity : 0.004 0.073 4094 Dihedral : 5.710 107.398 3196 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 2.32 % Allowed : 19.81 % Favored : 77.87 % 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: 1.83 (0.16), residues: 2844 helix: 2.27 (0.13), residues: 1596 sheet: -0.42 (0.35), residues: 224 loop : -0.05 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1523 HIS 0.009 0.001 HIS A2932 PHE 0.054 0.001 PHE A2635 TYR 0.038 0.001 TYR A2901 ARG 0.006 0.000 ARG A3585 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 1303) hydrogen bonds : angle 3.81506 ( 3813) covalent geometry : bond 0.00271 (23611) covalent geometry : angle 0.55444 (32029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 2.459 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: A 1463 LEU cc_start: 0.8047 (mt) cc_final: 0.7679 (pp) REVERT: A 1607 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5514 (tt) REVERT: A 1651 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: A 1941 MET cc_start: 0.8120 (tpp) cc_final: 0.7826 (tpp) REVERT: A 2779 MET cc_start: 0.8440 (mpp) cc_final: 0.8073 (mpp) REVERT: A 3199 MET cc_start: 0.6535 (tmm) cc_final: 0.6169 (tmm) REVERT: A 3527 ASN cc_start: 0.8241 (t0) cc_final: 0.8007 (t0) REVERT: A 3947 LEU cc_start: 0.8664 (tp) cc_final: 0.8442 (tp) REVERT: A 4065 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: A 4459 ILE cc_start: 0.9160 (mm) cc_final: 0.8880 (mp) REVERT: A 4617 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 4623 ASP cc_start: 0.7727 (m-30) cc_final: 0.7094 (p0) outliers start: 59 outliers final: 42 residues processed: 314 average time/residue: 0.3352 time to fit residues: 169.8253 Evaluate side-chains 297 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2520 ARG Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 159 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.143648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108205 restraints weight = 45812.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112015 restraints weight = 22143.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114502 restraints weight = 14468.488| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23611 Z= 0.115 Angle : 0.572 10.189 32029 Z= 0.279 Chirality : 0.040 0.178 3603 Planarity : 0.004 0.055 4094 Dihedral : 5.716 107.976 3196 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 20.83 % Favored : 77.20 % 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: 1.84 (0.16), residues: 2844 helix: 2.27 (0.13), residues: 1595 sheet: -0.38 (0.35), residues: 224 loop : -0.04 (0.21), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1523 HIS 0.008 0.001 HIS A2932 PHE 0.054 0.001 PHE A2635 TYR 0.038 0.001 TYR A2901 ARG 0.003 0.000 ARG A2836 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 1303) hydrogen bonds : angle 3.80367 ( 3813) covalent geometry : bond 0.00255 (23611) covalent geometry : angle 0.57197 (32029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 2.465 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: A 1463 LEU cc_start: 0.8061 (mt) cc_final: 0.7547 (pp) REVERT: A 1607 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5660 (tt) REVERT: A 1651 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7875 (mm-40) REVERT: A 1941 MET cc_start: 0.8114 (tpp) cc_final: 0.7836 (tpp) REVERT: A 2779 MET cc_start: 0.8352 (mpp) cc_final: 0.8000 (mpp) REVERT: A 2930 GLN cc_start: 0.5895 (mm-40) cc_final: 0.4996 (tt0) REVERT: A 2994 MET cc_start: 0.7290 (ppp) cc_final: 0.7086 (ppp) REVERT: A 3527 ASN cc_start: 0.8193 (t0) cc_final: 0.7981 (t0) REVERT: A 3712 CYS cc_start: 0.7968 (m) cc_final: 0.7381 (m) REVERT: A 3947 LEU cc_start: 0.8675 (tp) cc_final: 0.8465 (tp) REVERT: A 4459 ILE cc_start: 0.9166 (mm) cc_final: 0.8884 (mp) REVERT: A 4617 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7317 (p0) REVERT: A 4623 ASP cc_start: 0.7709 (m-30) cc_final: 0.7083 (p0) outliers start: 50 outliers final: 38 residues processed: 306 average time/residue: 0.3287 time to fit residues: 162.9833 Evaluate side-chains 297 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2865 LYS Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3181 ASN Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 161 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN A4404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.140426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104774 restraints weight = 45902.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108426 restraints weight = 22446.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110799 restraints weight = 14793.747| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23611 Z= 0.192 Angle : 0.622 10.239 32029 Z= 0.307 Chirality : 0.042 0.194 3603 Planarity : 0.004 0.047 4094 Dihedral : 5.757 106.281 3196 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 2.16 % Allowed : 20.48 % Favored : 77.36 % 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: 1.71 (0.16), residues: 2844 helix: 2.14 (0.13), residues: 1600 sheet: -0.39 (0.34), residues: 237 loop : -0.07 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A1523 HIS 0.010 0.001 HIS A2932 PHE 0.051 0.002 PHE A2635 TYR 0.036 0.002 TYR A2901 ARG 0.008 0.000 ARG A3060 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 1303) hydrogen bonds : angle 3.97931 ( 3813) covalent geometry : bond 0.00448 (23611) covalent geometry : angle 0.62233 (32029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 2.532 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 1607 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5331 (tt) REVERT: A 1651 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: A 2105 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.7052 (mtm110) REVERT: A 3712 CYS cc_start: 0.8152 (m) cc_final: 0.7176 (m) REVERT: A 4043 MET cc_start: 0.7787 (mmt) cc_final: 0.7536 (mmt) REVERT: A 4192 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7729 (mt-10) REVERT: A 4459 ILE cc_start: 0.9193 (mm) cc_final: 0.8704 (mp) REVERT: A 4623 ASP cc_start: 0.7796 (m-30) cc_final: 0.7102 (p0) outliers start: 55 outliers final: 44 residues processed: 290 average time/residue: 0.3299 time to fit residues: 156.5529 Evaluate side-chains 287 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 228 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 273 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 207 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN A4381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106705 restraints weight = 45871.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.110410 restraints weight = 22314.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112834 restraints weight = 14680.210| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23611 Z= 0.132 Angle : 0.587 11.647 32029 Z= 0.289 Chirality : 0.041 0.213 3603 Planarity : 0.004 0.068 4094 Dihedral : 5.761 107.057 3196 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 20.91 % Favored : 77.08 % 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: 1.80 (0.16), residues: 2844 helix: 2.20 (0.13), residues: 1592 sheet: -0.37 (0.35), residues: 222 loop : 0.01 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1523 HIS 0.012 0.001 HIS A2932 PHE 0.053 0.001 PHE A2635 TYR 0.043 0.001 TYR A2901 ARG 0.009 0.000 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1303) hydrogen bonds : angle 3.90759 ( 3813) covalent geometry : bond 0.00301 (23611) covalent geometry : angle 0.58665 (32029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 2.630 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 1607 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5509 (tt) REVERT: A 1651 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: A 1941 MET cc_start: 0.8389 (tpp) cc_final: 0.8084 (tpp) REVERT: A 2779 MET cc_start: 0.8319 (mpp) cc_final: 0.8065 (mpp) REVERT: A 3527 ASN cc_start: 0.8203 (t0) cc_final: 0.7977 (t0) REVERT: A 3712 CYS cc_start: 0.7735 (m) cc_final: 0.7218 (m) REVERT: A 3805 SER cc_start: 0.8804 (m) cc_final: 0.8392 (t) REVERT: A 4043 MET cc_start: 0.7661 (mmt) cc_final: 0.7415 (mmt) REVERT: A 4192 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7674 (mt-10) REVERT: A 4617 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (p0) REVERT: A 4623 ASP cc_start: 0.7706 (m-30) cc_final: 0.7071 (p0) outliers start: 51 outliers final: 41 residues processed: 287 average time/residue: 0.3297 time to fit residues: 153.5246 Evaluate side-chains 286 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3181 ASN Chi-restraints excluded: chain A residue 3188 HIS Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 150 optimal weight: 7.9990 chunk 280 optimal weight: 0.7980 chunk 208 optimal weight: 0.0040 chunk 223 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3181 ASN A4381 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.152808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120625 restraints weight = 47361.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.122508 restraints weight = 23559.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123125 restraints weight = 15548.988| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23611 Z= 0.137 Angle : 0.598 13.154 32029 Z= 0.293 Chirality : 0.041 0.209 3603 Planarity : 0.004 0.048 4094 Dihedral : 5.754 106.783 3196 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 1.77 % Allowed : 21.07 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.16), residues: 2844 helix: 2.17 (0.13), residues: 1594 sheet: -0.35 (0.35), residues: 222 loop : 0.01 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1523 HIS 0.012 0.001 HIS A2932 PHE 0.053 0.001 PHE A2635 TYR 0.025 0.001 TYR A2901 ARG 0.010 0.000 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1303) hydrogen bonds : angle 3.90576 ( 3813) covalent geometry : bond 0.00315 (23611) covalent geometry : angle 0.59790 (32029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7710.34 seconds wall clock time: 135 minutes 27.20 seconds (8127.20 seconds total)