Starting phenix.real_space_refine on Fri Jun 20 08:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.map" model { file = "/net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dh9_46860/06_2025/9dh9_46860.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 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 220 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23113 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: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 119 Unusual residues: {' MG': 3, 'ADP': 2, 'ANP': 1, 'ATP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 12.93, per 1000 atoms: 0.56 Number of scatterers: 23113 At special positions: 0 Unit cell: (118.045, 165.494, 153.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 10 15.00 Mg 3 11.99 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: 5.67 Conformation dependent library (CDL) restraints added in 2.8 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 21 sheets defined 61.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 1460 through 1472 Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.650A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.042A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 4.023A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.539A pdb=" N LEU A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.892A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.585A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.549A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.519A 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: 3.570A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1825 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 3.720A pdb=" N MET A1941 " --> pdb=" O ASP A1937 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.778A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1991 removed outlier: 3.849A pdb=" N ASP A1991 " --> pdb=" O PRO A1988 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 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: 4.282A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 4.130A 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: 3.942A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.592A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 4.246A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (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 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2558 through 2562 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.947A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.609A pdb=" N PHE A2606 " --> pdb=" O THR A2602 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.110A 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 2765 Proline residue: A2760 - end of helix removed outlier: 3.572A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2783 removed outlier: 3.695A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.951A 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 removed outlier: 3.573A pdb=" N TYR A2892 " --> pdb=" O GLU A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.711A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.505A 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 3006 through 3014 removed outlier: 3.519A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 removed outlier: 3.704A pdb=" N LEU A3020 " --> pdb=" O VAL A3017 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A3021 " --> pdb=" O PRO A3018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3017 through 3021' 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: 3.993A 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: 3.625A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.170A 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: 3.758A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 removed outlier: 3.821A 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 Processing helix chain 'A' and resid 3618 through 3630 removed outlier: 3.576A 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: 3.806A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3736 removed outlier: 4.036A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A3736 " --> pdb=" O LEU A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 Processing helix chain 'A' and resid 3762 through 3786 Processing helix chain 'A' and resid 3786 through 3801 Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.683A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.555A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.992A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 6.048A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.147A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.594A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) 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 4014 Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 4.253A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 4.036A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4091 removed outlier: 4.271A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.752A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.555A 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: 3.619A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.089A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.555A 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 removed outlier: 3.504A pdb=" N GLN A4262 " --> pdb=" O ASN A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.552A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A4279 " --> pdb=" O ARG A4276 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.600A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4346 removed outlier: 3.521A pdb=" N MET A4346 " --> pdb=" O LYS A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.772A 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 4499 Processing helix chain 'A' and resid 4500 through 4505 removed outlier: 3.569A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4500 through 4505' 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 4631 through 4638 removed outlier: 3.540A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.828A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1665 removed outlier: 3.604A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.625A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.535A 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: 6.426A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.434A 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: 6.116A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.326A 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 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2344 through 2345 removed outlier: 7.799A pdb=" N VAL A2345 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET A2222 " --> pdb=" O VAL A2345 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA9, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AB1, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB2, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB3, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 6.115A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A2664 " --> pdb=" O VAL A2618 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A2620 " --> pdb=" O ASP A2664 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A2734 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 3.827A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.703A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 5.958A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A3090 " --> pdb=" O HIS A2932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 5.871A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3662 through 3664 Processing sheet with id=AB9, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 5.920A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 3.926A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS A4287 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS A4292 " --> pdb=" O LYS A4287 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4539 through 4546 Processing sheet with id=AC3, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.723A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1293 hydrogen bonds defined for protein. 3783 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: 14.74 Time building geometry restraints manager: 6.79 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: 7534 1.34 - 1.46: 3829 1.46 - 1.58: 12035 1.58 - 1.70: 21 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 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O5' ANP A4703 " pdb=" PA ANP A4703 " ideal model delta sigma weight residual 1.655 1.575 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N ILE A2793 " pdb=" CA ILE A2793 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.10e+01 bond pdb=" N ARG A2811 " pdb=" CA ARG A2811 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.08e+01 ... (remaining 23606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 31793 3.89 - 7.77: 220 7.77 - 11.66: 15 11.66 - 15.55: 0 15.55 - 19.43: 1 Bond angle restraints: 32029 Sorted by residual: angle pdb=" CA PRO A2533 " pdb=" N PRO A2533 " pdb=" CD PRO A2533 " ideal model delta sigma weight residual 112.00 101.03 10.97 1.40e+00 5.10e-01 6.14e+01 angle pdb=" PB ANP A4703 " pdb=" N3B ANP A4703 " pdb=" PG ANP A4703 " ideal model delta sigma weight residual 126.95 107.52 19.43 3.00e+00 1.11e-01 4.20e+01 angle pdb=" CA PRO A2718 " pdb=" N PRO A2718 " pdb=" CD PRO A2718 " ideal model delta sigma weight residual 112.00 103.62 8.38 1.40e+00 5.10e-01 3.58e+01 angle pdb=" C TYR A3125 " pdb=" N MET A3126 " pdb=" CA MET A3126 " ideal model delta sigma weight residual 123.10 128.55 -5.45 9.60e-01 1.09e+00 3.23e+01 angle pdb=" CA PRO A2859 " pdb=" N PRO A2859 " pdb=" CD PRO A2859 " ideal model delta sigma weight residual 112.00 104.24 7.76 1.40e+00 5.10e-01 3.08e+01 ... (remaining 32024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 12915 20.88 - 41.75: 1209 41.75 - 62.63: 139 62.63 - 83.51: 50 83.51 - 104.38: 10 Dihedral angle restraints: 14323 sinusoidal: 5952 harmonic: 8371 Sorted by residual: 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 15.25 -75.24 1 2.00e+01 2.50e-03 1.79e+01 dihedral pdb=" CA CYS A2359 " pdb=" C CYS A2359 " pdb=" N GLY A2360 " pdb=" CA GLY A2360 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" O1A ANP A4703 " pdb=" O3A ANP A4703 " pdb=" PA ANP A4703 " pdb=" PB ANP A4703 " ideal model delta sinusoidal sigma weight residual 83.11 -21.27 104.38 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 14320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2758 0.049 - 0.098: 674 0.098 - 0.147: 150 0.147 - 0.197: 18 0.197 - 0.246: 3 Chirality restraints: 3603 Sorted by residual: 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 -2.60 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL A2568 " pdb=" N VAL A2568 " pdb=" C VAL A2568 " pdb=" CB VAL A2568 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL A2223 " pdb=" N VAL A2223 " pdb=" C VAL A2223 " pdb=" CB VAL A2223 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3600 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A2532 " 0.078 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A2533 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A2533 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A2533 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A3117 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A3118 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A3118 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A3118 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2717 " -0.065 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO A2718 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A2718 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2718 " -0.051 5.00e-02 4.00e+02 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 172 2.54 - 3.13: 18738 3.13 - 3.72: 36750 3.72 - 4.31: 50092 4.31 - 4.90: 84092 Nonbonded interactions: 189844 Sorted by model distance: nonbonded pdb=" O3G ANP A4703 " pdb="MG MG A4707 " model vdw 1.955 2.170 nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4706 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR A2602 " pdb="MG MG A4707 " model vdw 1.978 2.170 nonbonded pdb=" OE1 GLU A3933 " pdb=" NH1 ARG A3937 " model vdw 2.033 3.120 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 2.089 2.170 ... (remaining 189839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 59.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.110 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.005 0.145 23611 Z= 0.239 Angle : 0.830 19.432 32029 Z= 0.446 Chirality : 0.046 0.246 3603 Planarity : 0.008 0.111 4094 Dihedral : 15.956 104.385 8883 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 0.24 % Allowed : 0.39 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2844 helix: 1.49 (0.13), residues: 1573 sheet: -0.65 (0.36), residues: 221 loop : -0.61 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A4376 HIS 0.019 0.001 HIS A2918 PHE 0.050 0.002 PHE A4410 TYR 0.032 0.002 TYR A3103 ARG 0.016 0.001 ARG A2298 Details of bonding type rmsd hydrogen bonds : bond 0.12463 ( 1293) hydrogen bonds : angle 5.52932 ( 3783) covalent geometry : bond 0.00506 (23611) covalent geometry : angle 0.82968 (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 456 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 450 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1531 MET cc_start: 0.7684 (tpp) cc_final: 0.7241 (ttm) REVERT: A 1966 ARG cc_start: 0.6694 (ptm-80) cc_final: 0.6362 (ttp80) REVERT: A 2855 LEU cc_start: 0.8212 (tp) cc_final: 0.7812 (tp) REVERT: A 4111 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7805 (mmtp) REVERT: A 4338 ASP cc_start: 0.7855 (m-30) cc_final: 0.7596 (m-30) outliers start: 6 outliers final: 1 residues processed: 453 average time/residue: 0.3666 time to fit residues: 257.6200 Evaluate side-chains 321 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2901 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0000 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 223 optimal weight: 0.0020 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1646 ASN A1748 GLN A1810 HIS A1985 HIS A2271 ASN A2464 GLN A2476 HIS A2491 GLN A2588 HIS A2637 HIS A2707 GLN ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3711 GLN A3931 GLN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4532 ASN A4566 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104687 restraints weight = 37197.026| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.09 r_work: 0.3153 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23611 Z= 0.142 Angle : 0.642 7.285 32029 Z= 0.323 Chirality : 0.042 0.187 3603 Planarity : 0.006 0.064 4094 Dihedral : 7.003 132.057 3196 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.57 % Allowed : 9.36 % Favored : 89.07 % 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: 1.13 (0.16), residues: 2844 helix: 1.82 (0.13), residues: 1585 sheet: -0.71 (0.33), residues: 251 loop : -0.53 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4376 HIS 0.015 0.001 HIS A2918 PHE 0.019 0.001 PHE A3054 TYR 0.024 0.002 TYR A2748 ARG 0.007 0.001 ARG A2298 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 1293) hydrogen bonds : angle 4.28562 ( 3783) covalent geometry : bond 0.00340 (23611) covalent geometry : angle 0.64239 (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 386 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1966 ARG cc_start: 0.7302 (ptm-80) cc_final: 0.6755 (ttp-110) REVERT: A 2215 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: A 2578 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: A 2855 LEU cc_start: 0.8328 (tp) cc_final: 0.7888 (pp) REVERT: A 3000 LEU cc_start: 0.7418 (mt) cc_final: 0.7204 (mp) REVERT: A 3043 MET cc_start: 0.5922 (mpp) cc_final: 0.4577 (mtm) REVERT: A 3491 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7328 (mttt) REVERT: A 3558 GLU cc_start: 0.8696 (pt0) cc_final: 0.8475 (pt0) REVERT: A 3713 LEU cc_start: 0.8870 (tp) cc_final: 0.8565 (tp) REVERT: A 4338 ASP cc_start: 0.8696 (m-30) cc_final: 0.8362 (m-30) REVERT: A 4410 PHE cc_start: 0.6777 (t80) cc_final: 0.6265 (t80) outliers start: 40 outliers final: 21 residues processed: 369 average time/residue: 0.3804 time to fit residues: 218.5505 Evaluate side-chains 323 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2169 GLN Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3522 GLN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3608 LYS Chi-restraints excluded: chain A residue 3774 LYS Chi-restraints excluded: chain A residue 4377 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 266 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1646 ASN A2485 GLN A2588 HIS ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN A3584 ASN A4012 ASN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103220 restraints weight = 37226.883| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.07 r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23611 Z= 0.136 Angle : 0.589 7.580 32029 Z= 0.294 Chirality : 0.041 0.180 3603 Planarity : 0.005 0.055 4094 Dihedral : 6.303 129.342 3194 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 1.77 % Allowed : 11.87 % Favored : 86.36 % 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: 1.31 (0.16), residues: 2844 helix: 1.96 (0.13), residues: 1595 sheet: -0.66 (0.33), residues: 251 loop : -0.47 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4376 HIS 0.009 0.001 HIS A2918 PHE 0.020 0.001 PHE A4613 TYR 0.016 0.001 TYR A2748 ARG 0.007 0.000 ARG A1488 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1293) hydrogen bonds : angle 4.08162 ( 3783) covalent geometry : bond 0.00329 (23611) covalent geometry : angle 0.58947 (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 369 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2269 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8168 (t0) REVERT: A 2273 ARG cc_start: 0.7746 (mmp80) cc_final: 0.7457 (mmp80) REVERT: A 2578 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: A 2696 SER cc_start: 0.9134 (t) cc_final: 0.8841 (p) REVERT: A 2855 LEU cc_start: 0.8353 (tp) cc_final: 0.8061 (tp) REVERT: A 2905 LEU cc_start: 0.8208 (tp) cc_final: 0.7882 (mt) REVERT: A 2953 MET cc_start: 0.8631 (mtt) cc_final: 0.8284 (mtt) REVERT: A 2994 MET cc_start: 0.6875 (ppp) cc_final: 0.6347 (ptt) REVERT: A 3043 MET cc_start: 0.6099 (mpp) cc_final: 0.4825 (mtm) REVERT: A 3491 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7312 (mttt) REVERT: A 3551 GLU cc_start: 0.7638 (pm20) cc_final: 0.7195 (pm20) REVERT: A 3572 LEU cc_start: 0.9361 (tp) cc_final: 0.9049 (tp) REVERT: A 3717 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 4220 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 4310 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 4338 ASP cc_start: 0.8619 (m-30) cc_final: 0.8241 (m-30) REVERT: A 4410 PHE cc_start: 0.6848 (t80) cc_final: 0.6250 (t80) REVERT: A 4414 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7116 (mp0) outliers start: 45 outliers final: 25 residues processed: 351 average time/residue: 0.3870 time to fit residues: 209.8492 Evaluate side-chains 322 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 ASP Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2169 GLN Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3608 LYS Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 105 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 272 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 269 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 274 optimal weight: 0.0030 chunk 180 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2215 GLN A2588 HIS ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** 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 = 0.3596 r_free = 0.3596 target = 0.127315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103212 restraints weight = 37634.380| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.09 r_work: 0.3131 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1886 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= 0.117 Angle : 0.559 6.978 32029 Z= 0.278 Chirality : 0.040 0.175 3603 Planarity : 0.005 0.053 4094 Dihedral : 5.996 124.968 3194 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 2.12 % Allowed : 13.33 % Favored : 84.55 % 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: 1.50 (0.16), residues: 2844 helix: 2.11 (0.13), residues: 1594 sheet: -0.65 (0.33), residues: 271 loop : -0.34 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4376 HIS 0.007 0.001 HIS A2918 PHE 0.015 0.001 PHE A3149 TYR 0.016 0.001 TYR A2748 ARG 0.007 0.000 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1293) hydrogen bonds : angle 3.94394 ( 3783) covalent geometry : bond 0.00273 (23611) covalent geometry : angle 0.55931 (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 361 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1651 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: A 2273 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7566 (mmp80) REVERT: A 2342 MET cc_start: 0.8858 (mtt) cc_final: 0.8558 (mtt) REVERT: A 2578 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: A 2696 SER cc_start: 0.9109 (t) cc_final: 0.8805 (p) REVERT: A 2855 LEU cc_start: 0.8362 (tp) cc_final: 0.8086 (tp) REVERT: A 2905 LEU cc_start: 0.8332 (tp) cc_final: 0.7958 (mt) REVERT: A 2910 VAL cc_start: 0.9273 (p) cc_final: 0.9020 (t) REVERT: A 2953 MET cc_start: 0.8636 (mtt) cc_final: 0.8400 (mtt) REVERT: A 2994 MET cc_start: 0.6836 (ppp) cc_final: 0.6604 (ptt) REVERT: A 3043 MET cc_start: 0.6178 (mpp) cc_final: 0.4910 (mtt) REVERT: A 3491 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7308 (mttt) REVERT: A 3728 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7897 (ttt-90) REVERT: A 4310 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 4338 ASP cc_start: 0.8568 (m-30) cc_final: 0.8182 (m-30) REVERT: A 4377 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.3922 (mtm) REVERT: A 4410 PHE cc_start: 0.6879 (t80) cc_final: 0.6335 (t80) REVERT: A 4414 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 4429 GLN cc_start: 0.7770 (pt0) cc_final: 0.7399 (pt0) REVERT: A 4481 ASP cc_start: 0.7675 (t70) cc_final: 0.7378 (t0) outliers start: 54 outliers final: 29 residues processed: 341 average time/residue: 0.3709 time to fit residues: 197.4793 Evaluate side-chains 321 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2373 MET Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3522 GLN Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3645 LEU Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4414 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 135 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 143 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN A3667 GLN A4100 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098837 restraints weight = 37420.100| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.01 r_work: 0.3054 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23611 Z= 0.161 Angle : 0.587 9.095 32029 Z= 0.292 Chirality : 0.041 0.234 3603 Planarity : 0.005 0.054 4094 Dihedral : 5.941 115.828 3194 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.36 % Allowed : 14.35 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.16), residues: 2844 helix: 2.11 (0.13), residues: 1595 sheet: -0.72 (0.33), residues: 271 loop : -0.27 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A4376 HIS 0.005 0.001 HIS A2918 PHE 0.022 0.002 PHE A4613 TYR 0.019 0.001 TYR A2748 ARG 0.009 0.001 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1293) hydrogen bonds : angle 3.97248 ( 3783) covalent geometry : bond 0.00393 (23611) covalent geometry : angle 0.58727 (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 352 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1855 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: A 1966 ARG cc_start: 0.7439 (ptm-80) cc_final: 0.6937 (ttp80) REVERT: A 2269 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8133 (t0) REVERT: A 2273 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7657 (mmp80) REVERT: A 2342 MET cc_start: 0.8937 (mtt) cc_final: 0.8650 (mtt) REVERT: A 2361 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8368 (ttp) REVERT: A 2578 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: A 2696 SER cc_start: 0.9106 (t) cc_final: 0.8780 (p) REVERT: A 2855 LEU cc_start: 0.8335 (tp) cc_final: 0.8133 (tp) REVERT: A 3043 MET cc_start: 0.6182 (mpp) cc_final: 0.4813 (mtp) REVERT: A 3491 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7316 (mttt) REVERT: A 3551 GLU cc_start: 0.7708 (pm20) cc_final: 0.7295 (pm20) REVERT: A 3654 ARG cc_start: 0.6972 (mtm110) cc_final: 0.6634 (mtm110) REVERT: A 3728 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7955 (ttt-90) REVERT: A 4023 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 4310 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 4410 PHE cc_start: 0.7015 (t80) cc_final: 0.6466 (t80) REVERT: A 4414 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7062 (mp0) outliers start: 60 outliers final: 34 residues processed: 331 average time/residue: 0.3929 time to fit residues: 202.4610 Evaluate side-chains 309 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3522 GLN Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4588 THR 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 227 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3880 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100007 restraints weight = 37192.257| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.08 r_work: 0.3075 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23611 Z= 0.129 Angle : 0.564 8.075 32029 Z= 0.279 Chirality : 0.040 0.201 3603 Planarity : 0.005 0.056 4094 Dihedral : 5.828 115.606 3194 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 2.04 % Allowed : 15.64 % 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: 1.63 (0.16), residues: 2844 helix: 2.18 (0.13), residues: 1593 sheet: -0.64 (0.33), residues: 261 loop : -0.21 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4376 HIS 0.006 0.001 HIS A2918 PHE 0.018 0.001 PHE A2682 TYR 0.018 0.001 TYR A2748 ARG 0.009 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 1293) hydrogen bonds : angle 3.91431 ( 3783) covalent geometry : bond 0.00310 (23611) covalent geometry : angle 0.56424 (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 342 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1855 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: A 1966 ARG cc_start: 0.7491 (ptm-80) cc_final: 0.6961 (ttp80) REVERT: A 2273 ARG cc_start: 0.7940 (mmp80) cc_final: 0.7707 (mmp80) REVERT: A 2295 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8560 (mt) REVERT: A 2342 MET cc_start: 0.8944 (mtt) cc_final: 0.8640 (mtt) REVERT: A 2361 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8365 (ttp) REVERT: A 2578 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: A 2603 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8430 (ttm) REVERT: A 2696 SER cc_start: 0.9117 (t) cc_final: 0.8795 (p) REVERT: A 2855 LEU cc_start: 0.8363 (tp) cc_final: 0.8134 (tp) REVERT: A 3043 MET cc_start: 0.6157 (mpp) cc_final: 0.5871 (mmp) REVERT: A 3491 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7391 (mttt) REVERT: A 3551 GLU cc_start: 0.7710 (pm20) cc_final: 0.7341 (pm20) REVERT: A 3728 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8002 (ttt-90) REVERT: A 4023 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: A 4310 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 4338 ASP cc_start: 0.8689 (m-30) cc_final: 0.8297 (m-30) outliers start: 52 outliers final: 37 residues processed: 325 average time/residue: 0.3868 time to fit residues: 194.7531 Evaluate side-chains 309 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3522 GLN Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3608 LYS Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4255 ARG Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4588 THR 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 6 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 0.0040 chunk 218 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 overall best weight: 0.7812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2171 HIS A2215 GLN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN A3880 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099720 restraints weight = 37302.584| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3064 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23611 Z= 0.131 Angle : 0.564 7.033 32029 Z= 0.279 Chirality : 0.040 0.204 3603 Planarity : 0.005 0.064 4094 Dihedral : 5.756 114.069 3194 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 2.36 % Allowed : 15.41 % Favored : 82.23 % 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: 1.65 (0.16), residues: 2844 helix: 2.18 (0.13), residues: 1603 sheet: -0.64 (0.34), residues: 261 loop : -0.20 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4376 HIS 0.005 0.001 HIS A2918 PHE 0.031 0.001 PHE A4410 TYR 0.018 0.001 TYR A2748 ARG 0.011 0.000 ARG A3923 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1293) hydrogen bonds : angle 3.90652 ( 3783) covalent geometry : bond 0.00313 (23611) covalent geometry : angle 0.56431 (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 337 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1855 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: A 1966 ARG cc_start: 0.7487 (ptm-80) cc_final: 0.6966 (ttp80) REVERT: A 2197 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8342 (tt0) REVERT: A 2215 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: A 2269 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8168 (t0) REVERT: A 2273 ARG cc_start: 0.7939 (mmp80) cc_final: 0.7548 (mmp80) REVERT: A 2361 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: A 2578 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: A 2696 SER cc_start: 0.9106 (t) cc_final: 0.8776 (p) REVERT: A 2855 LEU cc_start: 0.8363 (tp) cc_final: 0.8135 (tp) REVERT: A 3032 GLN cc_start: 0.7719 (mt0) cc_final: 0.7510 (mt0) REVERT: A 3043 MET cc_start: 0.6163 (mpp) cc_final: 0.5905 (mmp) REVERT: A 3491 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7387 (mttt) REVERT: A 3551 GLU cc_start: 0.7738 (pm20) cc_final: 0.7423 (pm20) REVERT: A 3728 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8019 (ttt-90) REVERT: A 4023 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 4310 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 4338 ASP cc_start: 0.8712 (m-30) cc_final: 0.8324 (m-30) REVERT: A 4410 PHE cc_start: 0.6465 (t80) cc_final: 0.5907 (t80) REVERT: A 4414 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7138 (mp0) outliers start: 60 outliers final: 38 residues processed: 319 average time/residue: 0.4295 time to fit residues: 213.4073 Evaluate side-chains 311 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3522 GLN Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4255 ARG Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4588 THR 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 144 optimal weight: 1.9990 chunk 255 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 221 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100965 restraints weight = 37242.642| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.98 r_work: 0.3091 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2553 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= 0.117 Angle : 0.568 11.303 32029 Z= 0.280 Chirality : 0.040 0.320 3603 Planarity : 0.005 0.070 4094 Dihedral : 5.695 113.616 3194 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 2.08 % Allowed : 16.19 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 2844 helix: 2.22 (0.13), residues: 1601 sheet: -0.61 (0.34), residues: 261 loop : -0.17 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A4376 HIS 0.005 0.001 HIS A2918 PHE 0.028 0.001 PHE A4410 TYR 0.017 0.001 TYR A2748 ARG 0.009 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 1293) hydrogen bonds : angle 3.86683 ( 3783) covalent geometry : bond 0.00275 (23611) covalent geometry : angle 0.56802 (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 332 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1639 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8439 (tt0) REVERT: A 1855 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: A 1966 ARG cc_start: 0.7446 (ptm-80) cc_final: 0.6923 (ttp80) REVERT: A 2197 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8255 (tt0) REVERT: A 2291 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8916 (t) REVERT: A 2295 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 2361 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8320 (ttp) REVERT: A 2578 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8291 (mm-30) REVERT: A 2696 SER cc_start: 0.9095 (t) cc_final: 0.8769 (p) REVERT: A 2855 LEU cc_start: 0.8364 (tp) cc_final: 0.8134 (tp) REVERT: A 3043 MET cc_start: 0.6205 (mpp) cc_final: 0.5977 (mmp) REVERT: A 3491 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7369 (mttt) REVERT: A 3551 GLU cc_start: 0.7683 (pm20) cc_final: 0.7383 (pm20) REVERT: A 3572 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 3728 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8004 (ttt-90) REVERT: A 3912 ASN cc_start: 0.8690 (t0) cc_final: 0.8141 (p0) REVERT: A 4023 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: A 4310 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 4338 ASP cc_start: 0.8683 (m-30) cc_final: 0.8311 (m-30) REVERT: A 4377 MET cc_start: 0.5189 (mmm) cc_final: 0.2553 (mtm) outliers start: 53 outliers final: 38 residues processed: 314 average time/residue: 0.3848 time to fit residues: 187.8764 Evaluate side-chains 311 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4255 ARG Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4455 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 3 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2215 GLN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099556 restraints weight = 37328.674| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.02 r_work: 0.3063 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23611 Z= 0.139 Angle : 0.583 9.147 32029 Z= 0.288 Chirality : 0.041 0.326 3603 Planarity : 0.005 0.070 4094 Dihedral : 5.707 112.735 3194 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 2.20 % Allowed : 16.08 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2844 helix: 2.18 (0.13), residues: 1600 sheet: -0.65 (0.34), residues: 262 loop : -0.16 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A4376 HIS 0.004 0.001 HIS A2463 PHE 0.037 0.001 PHE A4410 TYR 0.019 0.001 TYR A2748 ARG 0.009 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1293) hydrogen bonds : angle 3.88632 ( 3783) covalent geometry : bond 0.00339 (23611) covalent geometry : angle 0.58349 (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 328 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1639 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8466 (tt0) REVERT: A 1855 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: A 1960 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9179 (t80) REVERT: A 2361 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: A 2578 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: A 2696 SER cc_start: 0.9022 (t) cc_final: 0.8776 (p) REVERT: A 2855 LEU cc_start: 0.8382 (tp) cc_final: 0.8150 (tp) REVERT: A 3043 MET cc_start: 0.6261 (mpp) cc_final: 0.6026 (mmp) REVERT: A 3491 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7374 (mttt) REVERT: A 3551 GLU cc_start: 0.7696 (pm20) cc_final: 0.7448 (pm20) REVERT: A 3572 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8813 (mp) REVERT: A 3728 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8052 (ttt-90) REVERT: A 3912 ASN cc_start: 0.8742 (t0) cc_final: 0.8191 (p0) REVERT: A 4023 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: A 4296 MET cc_start: 0.9297 (tpt) cc_final: 0.8935 (tpt) REVERT: A 4310 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 4338 ASP cc_start: 0.8758 (m-30) cc_final: 0.8380 (m-30) REVERT: A 4410 PHE cc_start: 0.6384 (t80) cc_final: 0.5804 (t80) REVERT: A 4414 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7125 (mp0) outliers start: 56 outliers final: 40 residues processed: 311 average time/residue: 0.4037 time to fit residues: 195.0600 Evaluate side-chains 305 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3186 LEU Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4255 ARG Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4455 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 109 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2215 GLN ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099241 restraints weight = 37635.847| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.03 r_work: 0.3063 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23611 Z= 0.138 Angle : 0.585 10.380 32029 Z= 0.287 Chirality : 0.041 0.319 3603 Planarity : 0.005 0.072 4094 Dihedral : 5.777 112.197 3194 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 1.97 % Allowed : 16.51 % Favored : 81.53 % 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: 1.66 (0.16), residues: 2844 helix: 2.17 (0.13), residues: 1601 sheet: -0.63 (0.34), residues: 261 loop : -0.15 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A4376 HIS 0.005 0.001 HIS A2463 PHE 0.038 0.001 PHE A4410 TYR 0.018 0.001 TYR A2748 ARG 0.009 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 1293) hydrogen bonds : angle 3.88661 ( 3783) covalent geometry : bond 0.00337 (23611) covalent geometry : angle 0.58501 (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 316 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1639 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8482 (tt0) REVERT: A 1855 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: A 2269 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8120 (t0) REVERT: A 2361 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8355 (ttp) REVERT: A 2578 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 2696 SER cc_start: 0.9024 (t) cc_final: 0.8789 (p) REVERT: A 2835 ASP cc_start: 0.8669 (p0) cc_final: 0.8466 (p0) REVERT: A 2855 LEU cc_start: 0.8403 (tp) cc_final: 0.8164 (tp) REVERT: A 2911 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 3043 MET cc_start: 0.6312 (mpp) cc_final: 0.6111 (mmp) REVERT: A 3491 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7387 (mttt) REVERT: A 3551 GLU cc_start: 0.7705 (pm20) cc_final: 0.7453 (pm20) REVERT: A 3572 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 3728 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8061 (ttt-90) REVERT: A 3912 ASN cc_start: 0.8739 (t0) cc_final: 0.8227 (p0) REVERT: A 3923 ARG cc_start: 0.6199 (ttm110) cc_final: 0.5926 (mtp85) REVERT: A 4023 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: A 4287 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7965 (mmtm) REVERT: A 4296 MET cc_start: 0.9307 (tpt) cc_final: 0.8953 (tpt) REVERT: A 4310 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: A 4338 ASP cc_start: 0.8751 (m-30) cc_final: 0.8412 (m-30) REVERT: A 4410 PHE cc_start: 0.6410 (t80) cc_final: 0.5849 (t80) REVERT: A 4414 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7115 (mp0) outliers start: 50 outliers final: 38 residues processed: 301 average time/residue: 0.4161 time to fit residues: 197.2757 Evaluate side-chains 307 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1651 GLN Chi-restraints excluded: chain A residue 1665 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2319 LEU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2478 ASP Chi-restraints excluded: chain A residue 2518 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3186 LEU Chi-restraints excluded: chain A residue 3558 GLU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4023 GLN Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4255 ARG Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4455 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 19 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 279 optimal weight: 0.0670 chunk 220 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3880 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099884 restraints weight = 37243.841| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.01 r_work: 0.3068 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23611 Z= 0.129 Angle : 0.583 10.509 32029 Z= 0.286 Chirality : 0.041 0.316 3603 Planarity : 0.005 0.073 4094 Dihedral : 5.767 111.193 3194 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 2.04 % Allowed : 16.51 % Favored : 81.45 % 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: 1.69 (0.16), residues: 2844 helix: 2.19 (0.13), residues: 1604 sheet: -0.62 (0.34), residues: 261 loop : -0.13 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A4376 HIS 0.004 0.001 HIS A2463 PHE 0.036 0.001 PHE A4410 TYR 0.021 0.001 TYR A4636 ARG 0.009 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1293) hydrogen bonds : angle 3.86925 ( 3783) covalent geometry : bond 0.00315 (23611) covalent geometry : angle 0.58300 (32029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13086.11 seconds wall clock time: 227 minutes 8.88 seconds (13628.88 seconds total)