Starting phenix.real_space_refine on Fri Sep 19 10:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e22_47429/09_2025/9e22_47429.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 1 5.21 5 S 112 5.16 5 C 15515 2.51 5 N 4324 2.21 5 O 4650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 22914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2925, 22914 Classifications: {'peptide': 2925} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 3, 'PTRANS': 127, 'TRANS': 2794} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 16, 'PHE:plan': 8, 'ARG:plan': 11, 'TRP:plan': 5, 'ASN:plan1': 7, 'TYR:plan': 6, 'ASP:plan': 10, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 351 Chain: "E" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1581 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1026 Unresolved non-hydrogen angles: 1321 Unresolved non-hydrogen dihedrals: 894 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLU:plan': 18, 'TRP:plan': 11, 'ARG:plan': 15, 'TYR:plan': 6, 'HIS:plan': 16, 'PHE:plan': 12, 'ASP:plan': 21, 'GLN:plan1': 6, 'ASN:plan1': 7, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 553 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.54, per 1000 atoms: 0.23 Number of scatterers: 24612 At special positions: 0 Unit cell: (118.745, 168.3, 168.3, 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 112 16.00 P 10 15.00 Mg 1 11.99 O 4650 8.00 N 4324 7.00 C 15515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6158 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 28 sheets defined 54.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 1449 through 1473 Processing helix chain 'A' and resid 1489 through 1508 Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.584A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A1553 " --> pdb=" O GLY A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1633 through 1643 removed outlier: 3.843A pdb=" N GLU A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1658 removed outlier: 4.162A pdb=" N HIS A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A1655 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS A1656 " --> pdb=" O LYS A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1730 removed outlier: 3.888A pdb=" N ALA A1730 " --> pdb=" O ILE A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.743A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.728A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 3.666A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.837A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2062 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 4.022A pdb=" N ASN A2130 " --> pdb=" O GLU A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.508A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.718A 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 2394 through 2399 removed outlier: 3.504A pdb=" N ARG A2398 " --> pdb=" O GLN A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 removed outlier: 4.188A pdb=" N GLN A2414 " --> pdb=" O SER A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.880A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.768A 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 2503 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 2571 through 2586 Processing helix chain 'A' and resid 2600 through 2611 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.119A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.295A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.854A 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 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2902 removed outlier: 4.108A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2945 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3004 through 3015 removed outlier: 3.522A pdb=" N MET A3008 " --> pdb=" O PHE A3004 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3082 through 3088 Processing helix chain 'A' and resid 3098 through 3111 removed outlier: 3.528A pdb=" N PHE A3109 " --> pdb=" O VAL A3105 " (cutoff:3.500A) Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.593A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3517 removed outlier: 3.719A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 removed outlier: 3.798A pdb=" N ARG A3582 " --> pdb=" O ILE A3578 " (cutoff:3.500A) Processing helix chain 'A' and resid 3595 through 3604 Processing helix chain 'A' and resid 3605 through 3608 removed outlier: 3.585A pdb=" N LYS A3608 " --> pdb=" O LYS A3605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3605 through 3608' Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3644 through 3651 removed outlier: 4.781A pdb=" N VAL A3648 " --> pdb=" O VAL A3644 " (cutoff:3.500A) Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.528A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3733 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 3.643A pdb=" N ASN A3754 " --> pdb=" O LEU A3750 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3765 through 3786 removed outlier: 3.724A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3800 Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.558A 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 3842 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 4.067A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 6.200A 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: 6.279A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 4.167A 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: 3.759A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.808A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.782A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.298A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.806A 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 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 removed outlier: 3.847A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.328A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4195 through 4197 No H-bonds generated for 'chain 'A' and resid 4195 through 4197' Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.635A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4289 through 4291 No H-bonds generated for 'chain 'A' and resid 4289 through 4291' Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 removed outlier: 4.183A pdb=" N LEU A4321 " --> pdb=" O THR A4317 " (cutoff:3.500A) Processing helix chain 'A' and resid 4326 through 4351 removed outlier: 3.585A pdb=" N LEU A4349 " --> pdb=" O LYS A4345 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A4351 " --> pdb=" O GLN A4347 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 removed outlier: 3.758A pdb=" N THR A4382 " --> pdb=" O ARG A4378 " (cutoff:3.500A) Processing helix chain 'A' and resid 4403 through 4406 removed outlier: 3.754A pdb=" N LYS A4406 " --> pdb=" O GLU A4403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4403 through 4406' Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4639 Processing helix chain 'E' and resid 289 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.182A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.603A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A1676 " --> pdb=" O VAL A1684 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1684 " --> pdb=" O ILE A1676 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 removed outlier: 3.628A pdb=" N MET A1861 " --> pdb=" O ALA A1864 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1904 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.941A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) 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 2220 through 2222 Processing sheet with id=AA8, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 7.234A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2267 through 2268 removed outlier: 3.700A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2324 through 2325 removed outlier: 3.850A pdb=" N LEU A2333 " --> pdb=" O LEU A2325 " (cutoff:3.500A) 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 2592 through 2594 Processing sheet with id=AB4, first strand: chain 'A' and resid 2615 through 2618 removed outlier: 6.099A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 3.568A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 7.173A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A3063 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A2994 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A3068 " --> pdb=" O LEU A2935 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3679 through 3680 removed outlier: 5.909A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.728A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.687A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4508 through 4510 Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 3.720A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.431A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A4607 " --> pdb=" O VAL A4622 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 96 through 104 removed outlier: 7.097A pdb=" N GLU E 100 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU E 408 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR E 102 " --> pdb=" O VAL E 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 116 removed outlier: 4.173A pdb=" N ARG E 113 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL E 134 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 158 removed outlier: 4.002A pdb=" N ASP E 155 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS E 168 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 166 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 173 through 178 removed outlier: 5.665A pdb=" N ASP E 178 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N CYS E 184 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 195 through 200 removed outlier: 3.656A pdb=" N SER E 197 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 199 " --> pdb=" O VAL E 208 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 215 through 217 Processing sheet with id=AC9, first strand: chain 'E' and resid 237 through 242 removed outlier: 7.165A pdb=" N CYS E 252 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL E 240 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA E 250 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 341 through 346 removed outlier: 3.690A pdb=" N LEU E 354 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 353 " --> pdb=" O TRP E 365 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 355 " --> pdb=" O ARG E 363 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 363 " --> pdb=" O SER E 355 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP E 366 " --> pdb=" O CYS E 372 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N CYS E 372 " --> pdb=" O ASP E 366 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 3.04 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: 8301 1.34 - 1.46: 4483 1.46 - 1.58: 12099 1.58 - 1.70: 16 1.70 - 1.81: 187 Bond restraints: 25086 Sorted by residual: bond pdb=" CA ASP A1937 " pdb=" CB ASP A1937 " ideal model delta sigma weight residual 1.527 1.568 -0.040 2.48e-02 1.63e+03 2.64e+00 bond pdb=" CA ILE A2154 " pdb=" C ILE A2154 " ideal model delta sigma weight residual 1.520 1.531 -0.012 8.80e-03 1.29e+04 1.77e+00 bond pdb=" C PHE A1626 " pdb=" O PHE A1626 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.63e+00 bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.331 1.346 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" N PHE A1629 " pdb=" CA PHE A1629 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.49e+00 ... (remaining 25081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 33404 1.88 - 3.75: 588 3.75 - 5.63: 92 5.63 - 7.51: 29 7.51 - 9.38: 10 Bond angle restraints: 34123 Sorted by residual: angle pdb=" N VAL A3129 " pdb=" CA VAL A3129 " pdb=" C VAL A3129 " ideal model delta sigma weight residual 113.42 109.28 4.14 1.17e+00 7.31e-01 1.25e+01 angle pdb=" C ARG A1628 " pdb=" N PHE A1629 " pdb=" CA PHE A1629 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CA ARG A2863 " pdb=" CB ARG A2863 " pdb=" CG ARG A2863 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASP A1669 " pdb=" N ASN A1670 " pdb=" CA ASN A1670 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C PRO A2859 " pdb=" N ASN A2860 " pdb=" CA ASN A2860 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 ... (remaining 34118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13493 17.92 - 35.83: 1367 35.83 - 53.75: 253 53.75 - 71.67: 44 71.67 - 89.58: 30 Dihedral angle restraints: 15187 sinusoidal: 5715 harmonic: 9472 Sorted by residual: dihedral pdb=" CA LEU A3020 " pdb=" C LEU A3020 " pdb=" N PHE A3021 " pdb=" CA PHE A3021 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA A3719 " pdb=" C ALA A3719 " pdb=" N GLU A3720 " pdb=" CA GLU A3720 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLU A1964 " pdb=" C GLU A1964 " pdb=" N GLU A1965 " pdb=" CA GLU A1965 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 15184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2492 0.034 - 0.068: 988 0.068 - 0.103: 316 0.103 - 0.137: 114 0.137 - 0.171: 7 Chirality restraints: 3917 Sorted by residual: chirality pdb=" CA VAL A2999 " pdb=" N VAL A2999 " pdb=" C VAL A2999 " pdb=" CB VAL A2999 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CB THR A3685 " pdb=" CA THR A3685 " pdb=" OG1 THR A3685 " pdb=" CG2 THR A3685 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA ILE A2154 " pdb=" N ILE A2154 " pdb=" C ILE A2154 " pdb=" CB ILE A2154 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 3914 not shown) Planarity restraints: 4441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A2717 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A2718 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A2718 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A2718 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2926 " 0.018 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE A2926 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A2926 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A2926 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A2926 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A2926 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A2926 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2668 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A2669 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A2669 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2669 " 0.029 5.00e-02 4.00e+02 ... (remaining 4438 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 27 2.65 - 3.21: 21904 3.21 - 3.77: 38959 3.77 - 4.34: 48814 4.34 - 4.90: 80881 Nonbonded interactions: 190585 Sorted by model distance: nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4703 " model vdw 2.085 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4703 " model vdw 2.094 2.170 nonbonded pdb=" O2' ADP A4705 " pdb=" O3' ADP A4705 " model vdw 2.497 2.432 nonbonded pdb=" O2' ADP A4701 " pdb=" O3' ADP A4701 " model vdw 2.500 2.432 nonbonded pdb=" O LEU A3645 " pdb=" CB LEU A3649 " model vdw 2.521 2.752 ... (remaining 190580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25086 Z= 0.137 Angle : 0.627 9.384 34123 Z= 0.319 Chirality : 0.043 0.171 3917 Planarity : 0.005 0.061 4441 Dihedral : 15.230 89.582 9029 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 3235 helix: 0.99 (0.12), residues: 1663 sheet: -0.87 (0.30), residues: 330 loop : -0.73 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4449 TYR 0.028 0.001 TYR A2496 PHE 0.039 0.002 PHE A2926 TRP 0.022 0.001 TRP A1701 HIS 0.005 0.001 HIS A3063 Details of bonding type rmsd covalent geometry : bond 0.00282 (25086) covalent geometry : angle 0.62723 (34123) hydrogen bonds : bond 0.10293 ( 1369) hydrogen bonds : angle 5.71850 ( 4038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2321 ASP cc_start: 0.7550 (t0) cc_final: 0.7016 (t0) REVERT: A 2505 ASP cc_start: 0.7299 (p0) cc_final: 0.6694 (p0) REVERT: A 2720 ARG cc_start: 0.7380 (mpt180) cc_final: 0.6587 (mmt90) REVERT: A 2770 THR cc_start: 0.8391 (m) cc_final: 0.8022 (p) REVERT: A 2863 ARG cc_start: 0.7777 (tpt90) cc_final: 0.7515 (tpt90) REVERT: A 2995 ASP cc_start: 0.8644 (t0) cc_final: 0.8185 (t70) REVERT: A 3006 GLU cc_start: 0.7920 (pm20) cc_final: 0.7646 (tp30) REVERT: A 3043 MET cc_start: 0.7341 (mmp) cc_final: 0.6787 (tpp) REVERT: A 3068 MET cc_start: 0.7238 (ppp) cc_final: 0.7033 (ppp) REVERT: A 3195 GLU cc_start: 0.7083 (tp30) cc_final: 0.6699 (tp30) REVERT: A 3199 MET cc_start: 0.5917 (tmm) cc_final: 0.5612 (tmm) REVERT: A 3641 TYR cc_start: 0.7708 (p90) cc_final: 0.7407 (p90) REVERT: A 3791 MET cc_start: 0.5510 (mmt) cc_final: 0.4380 (tmm) REVERT: A 3923 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8176 (mmm160) REVERT: A 4129 GLU cc_start: 0.8163 (mp0) cc_final: 0.7883 (mp0) REVERT: A 4217 ASP cc_start: 0.8325 (t70) cc_final: 0.8031 (t0) REVERT: A 4348 MET cc_start: 0.8187 (mtm) cc_final: 0.7578 (ptm) REVERT: A 4410 PHE cc_start: 0.7505 (t80) cc_final: 0.7254 (t80) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1489 time to fit residues: 79.2943 Evaluate side-chains 246 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 50.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN ** A2083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2964 HIS A3155 HIS A4466 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.162354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123963 restraints weight = 50790.276| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.01 r_work: 0.3694 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25086 Z= 0.113 Angle : 0.519 8.284 34123 Z= 0.258 Chirality : 0.040 0.220 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.146 85.795 3575 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 1.11 % Allowed : 8.34 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.15), residues: 3235 helix: 1.56 (0.13), residues: 1675 sheet: -0.65 (0.30), residues: 331 loop : -0.67 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2869 TYR 0.020 0.001 TYR A2892 PHE 0.022 0.001 PHE A3629 TRP 0.021 0.001 TRP A2500 HIS 0.008 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00246 (25086) covalent geometry : angle 0.51860 (34123) hydrogen bonds : bond 0.03640 ( 1369) hydrogen bonds : angle 4.65297 ( 4038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.968 Fit side-chains REVERT: A 1658 PHE cc_start: 0.5964 (m-80) cc_final: 0.5593 (m-10) REVERT: A 1677 SER cc_start: 0.8042 (m) cc_final: 0.7764 (t) REVERT: A 1937 ASP cc_start: 0.8084 (p0) cc_final: 0.7854 (p0) REVERT: A 1976 GLN cc_start: 0.8637 (tt0) cc_final: 0.8408 (mt0) REVERT: A 2045 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7798 (t0) REVERT: A 2221 MET cc_start: 0.7599 (mtt) cc_final: 0.7309 (mtt) REVERT: A 2321 ASP cc_start: 0.7619 (t0) cc_final: 0.7342 (t0) REVERT: A 2770 THR cc_start: 0.8377 (m) cc_final: 0.8018 (p) REVERT: A 3043 MET cc_start: 0.7303 (mmp) cc_final: 0.6764 (tpp) REVERT: A 3195 GLU cc_start: 0.7109 (tp30) cc_final: 0.6729 (tp30) REVERT: A 3199 MET cc_start: 0.6043 (tmm) cc_final: 0.5736 (tmm) REVERT: A 3641 TYR cc_start: 0.7747 (p90) cc_final: 0.7448 (p90) REVERT: A 3694 SER cc_start: 0.8691 (t) cc_final: 0.8134 (p) REVERT: A 3791 MET cc_start: 0.5539 (mmt) cc_final: 0.4436 (tmm) REVERT: A 4129 GLU cc_start: 0.8275 (mp0) cc_final: 0.8007 (mp0) REVERT: A 4217 ASP cc_start: 0.8424 (t70) cc_final: 0.8142 (t0) REVERT: A 4348 MET cc_start: 0.7893 (mtm) cc_final: 0.7448 (ptm) REVERT: A 4386 ASN cc_start: 0.9047 (m-40) cc_final: 0.8820 (m-40) REVERT: A 4537 GLU cc_start: 0.6989 (tp30) cc_final: 0.6685 (tp30) outliers start: 27 outliers final: 12 residues processed: 283 average time/residue: 0.1561 time to fit residues: 72.8945 Evaluate side-chains 255 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 207 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1876 GLN A2134 GLN A3063 HIS A4098 ASN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 ASN ** 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 = 0.4401 r_free = 0.4401 target = 0.159469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118625 restraints weight = 50561.201| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.37 r_work: 0.3689 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25086 Z= 0.165 Angle : 0.553 11.509 34123 Z= 0.277 Chirality : 0.041 0.191 3917 Planarity : 0.004 0.057 4441 Dihedral : 6.220 88.905 3575 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.48 % Allowed : 10.89 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 3235 helix: 1.66 (0.13), residues: 1677 sheet: -0.76 (0.29), residues: 345 loop : -0.59 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1679 TYR 0.020 0.001 TYR A2496 PHE 0.021 0.002 PHE A3629 TRP 0.038 0.001 TRP A2500 HIS 0.016 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00378 (25086) covalent geometry : angle 0.55275 (34123) hydrogen bonds : bond 0.03823 ( 1369) hydrogen bonds : angle 4.51683 ( 4038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 1658 PHE cc_start: 0.6158 (m-80) cc_final: 0.5643 (m-10) REVERT: A 1677 SER cc_start: 0.8101 (m) cc_final: 0.7835 (t) REVERT: A 1937 ASP cc_start: 0.8031 (p0) cc_final: 0.7821 (p0) REVERT: A 2045 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 2770 THR cc_start: 0.8440 (m) cc_final: 0.8050 (p) REVERT: A 2863 ARG cc_start: 0.7534 (tpt90) cc_final: 0.7321 (tpt90) REVERT: A 3030 MET cc_start: 0.6053 (mmm) cc_final: 0.5762 (mmm) REVERT: A 3043 MET cc_start: 0.7352 (mmp) cc_final: 0.6731 (tpp) REVERT: A 3195 GLU cc_start: 0.7288 (tp30) cc_final: 0.6889 (tp30) REVERT: A 3199 MET cc_start: 0.5873 (tmm) cc_final: 0.5568 (tmm) REVERT: A 3641 TYR cc_start: 0.7796 (p90) cc_final: 0.7496 (p90) REVERT: A 3694 SER cc_start: 0.8726 (t) cc_final: 0.8130 (p) REVERT: A 4098 ASN cc_start: 0.8676 (p0) cc_final: 0.8428 (p0) REVERT: A 4217 ASP cc_start: 0.8377 (t70) cc_final: 0.8110 (t0) REVERT: A 4348 MET cc_start: 0.7961 (mtm) cc_final: 0.7488 (ptm) REVERT: A 4386 ASN cc_start: 0.9109 (m-40) cc_final: 0.8860 (m-40) REVERT: A 4537 GLU cc_start: 0.6735 (tp30) cc_final: 0.6485 (tp30) outliers start: 36 outliers final: 22 residues processed: 272 average time/residue: 0.1567 time to fit residues: 71.2974 Evaluate side-chains 255 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3839 VAL Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 55 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 14 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3155 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 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 = 0.4416 r_free = 0.4416 target = 0.160767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.120117 restraints weight = 50336.311| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.39 r_work: 0.3711 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25086 Z= 0.110 Angle : 0.510 10.342 34123 Z= 0.252 Chirality : 0.040 0.293 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.121 87.728 3575 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.19 % Allowed : 13.15 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.15), residues: 3235 helix: 1.82 (0.13), residues: 1676 sheet: -0.68 (0.29), residues: 336 loop : -0.50 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2869 TYR 0.017 0.001 TYR A2496 PHE 0.021 0.001 PHE A3629 TRP 0.022 0.001 TRP A2845 HIS 0.005 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00242 (25086) covalent geometry : angle 0.50986 (34123) hydrogen bonds : bond 0.03536 ( 1369) hydrogen bonds : angle 4.34260 ( 4038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.915 Fit side-chains REVERT: A 1658 PHE cc_start: 0.6006 (m-80) cc_final: 0.5596 (m-10) REVERT: A 1677 SER cc_start: 0.8016 (m) cc_final: 0.7760 (t) REVERT: A 1937 ASP cc_start: 0.8031 (p0) cc_final: 0.7808 (p0) REVERT: A 2045 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7780 (t0) REVERT: A 2606 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 2770 THR cc_start: 0.8427 (m) cc_final: 0.8032 (p) REVERT: A 3030 MET cc_start: 0.6095 (mmm) cc_final: 0.5798 (mmm) REVERT: A 3043 MET cc_start: 0.7331 (mmp) cc_final: 0.6776 (tpp) REVERT: A 3195 GLU cc_start: 0.7244 (tp30) cc_final: 0.6844 (tp30) REVERT: A 3199 MET cc_start: 0.5853 (tmm) cc_final: 0.5575 (tmm) REVERT: A 3641 TYR cc_start: 0.7821 (p90) cc_final: 0.7400 (p90) REVERT: A 3694 SER cc_start: 0.8713 (t) cc_final: 0.8135 (p) REVERT: A 4098 ASN cc_start: 0.8704 (p0) cc_final: 0.8414 (p0) REVERT: A 4129 GLU cc_start: 0.8272 (mp0) cc_final: 0.8002 (mp0) REVERT: A 4217 ASP cc_start: 0.8374 (t70) cc_final: 0.8106 (t0) REVERT: A 4223 LEU cc_start: 0.8379 (mt) cc_final: 0.7694 (mt) REVERT: A 4346 MET cc_start: 0.8686 (mmt) cc_final: 0.8146 (mmt) REVERT: A 4348 MET cc_start: 0.7938 (mtm) cc_final: 0.7517 (ptm) REVERT: A 4386 ASN cc_start: 0.9086 (m-40) cc_final: 0.8841 (m-40) REVERT: A 4537 GLU cc_start: 0.6839 (tp30) cc_final: 0.6586 (tp30) outliers start: 29 outliers final: 18 residues processed: 274 average time/residue: 0.1370 time to fit residues: 63.6407 Evaluate side-chains 259 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 233 optimal weight: 0.4980 chunk 226 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 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 = 0.4422 r_free = 0.4422 target = 0.161309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.120771 restraints weight = 50480.859| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.41 r_work: 0.3724 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25086 Z= 0.100 Angle : 0.505 11.367 34123 Z= 0.249 Chirality : 0.039 0.267 3917 Planarity : 0.003 0.052 4441 Dihedral : 6.005 83.415 3575 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.44 % Allowed : 14.26 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3235 helix: 1.90 (0.13), residues: 1671 sheet: -0.64 (0.29), residues: 329 loop : -0.47 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2507 TYR 0.016 0.001 TYR A2748 PHE 0.041 0.001 PHE A4413 TRP 0.031 0.001 TRP A2500 HIS 0.003 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00217 (25086) covalent geometry : angle 0.50492 (34123) hydrogen bonds : bond 0.03423 ( 1369) hydrogen bonds : angle 4.26087 ( 4038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1658 PHE cc_start: 0.5972 (m-80) cc_final: 0.5538 (m-10) REVERT: A 1677 SER cc_start: 0.8023 (m) cc_final: 0.7763 (t) REVERT: A 2045 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7769 (t0) REVERT: A 2606 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 2770 THR cc_start: 0.8406 (m) cc_final: 0.8012 (p) REVERT: A 3043 MET cc_start: 0.7333 (mmp) cc_final: 0.6772 (tpp) REVERT: A 3091 LEU cc_start: 0.8891 (tt) cc_final: 0.8657 (tt) REVERT: A 3195 GLU cc_start: 0.7230 (tp30) cc_final: 0.6829 (tp30) REVERT: A 3199 MET cc_start: 0.5851 (tmm) cc_final: 0.5581 (tmm) REVERT: A 3586 TYR cc_start: 0.7751 (m-80) cc_final: 0.7235 (m-80) REVERT: A 3641 TYR cc_start: 0.7837 (p90) cc_final: 0.7447 (p90) REVERT: A 3694 SER cc_start: 0.8709 (t) cc_final: 0.8138 (p) REVERT: A 3791 MET cc_start: 0.5373 (mmt) cc_final: 0.3861 (tmm) REVERT: A 4098 ASN cc_start: 0.8667 (p0) cc_final: 0.8356 (p0) REVERT: A 4129 GLU cc_start: 0.8256 (mp0) cc_final: 0.7989 (mp0) REVERT: A 4217 ASP cc_start: 0.8363 (t70) cc_final: 0.8103 (t0) REVERT: A 4348 MET cc_start: 0.7949 (mtm) cc_final: 0.7529 (ptm) REVERT: A 4386 ASN cc_start: 0.9086 (m-40) cc_final: 0.8843 (m-40) REVERT: A 4537 GLU cc_start: 0.6832 (tp30) cc_final: 0.6589 (tp30) outliers start: 35 outliers final: 25 residues processed: 275 average time/residue: 0.1556 time to fit residues: 72.0094 Evaluate side-chains 272 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 3031 THR Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 139 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN A3155 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 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 = 0.4393 r_free = 0.4393 target = 0.158951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.118151 restraints weight = 50777.192| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.38 r_work: 0.3682 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25086 Z= 0.152 Angle : 0.536 10.469 34123 Z= 0.267 Chirality : 0.040 0.270 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.128 87.226 3575 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 14.71 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3235 helix: 1.86 (0.13), residues: 1674 sheet: -0.77 (0.29), residues: 340 loop : -0.44 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3078 TYR 0.021 0.001 TYR A2496 PHE 0.053 0.002 PHE A4413 TRP 0.030 0.001 TRP A2500 HIS 0.007 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00351 (25086) covalent geometry : angle 0.53578 (34123) hydrogen bonds : bond 0.03654 ( 1369) hydrogen bonds : angle 4.30092 ( 4038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1658 PHE cc_start: 0.6173 (m-80) cc_final: 0.5500 (m-10) REVERT: A 1677 SER cc_start: 0.8221 (m) cc_final: 0.7958 (t) REVERT: A 2045 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 2606 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7376 (t80) REVERT: A 2770 THR cc_start: 0.8427 (m) cc_final: 0.8044 (p) REVERT: A 3030 MET cc_start: 0.6163 (mmm) cc_final: 0.5954 (mmm) REVERT: A 3043 MET cc_start: 0.7277 (mmp) cc_final: 0.6782 (tpp) REVERT: A 3091 LEU cc_start: 0.8821 (tt) cc_final: 0.8563 (tt) REVERT: A 3164 ARG cc_start: 0.6861 (mtt180) cc_final: 0.6336 (mtp180) REVERT: A 3195 GLU cc_start: 0.7330 (tp30) cc_final: 0.6925 (tp30) REVERT: A 3199 MET cc_start: 0.5787 (tmm) cc_final: 0.5507 (tmm) REVERT: A 3586 TYR cc_start: 0.7838 (m-80) cc_final: 0.7359 (m-80) REVERT: A 3641 TYR cc_start: 0.7835 (p90) cc_final: 0.7421 (p90) REVERT: A 3677 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 3791 MET cc_start: 0.5437 (mmt) cc_final: 0.3903 (tmm) REVERT: A 4098 ASN cc_start: 0.8715 (p0) cc_final: 0.8396 (p0) REVERT: A 4217 ASP cc_start: 0.8375 (t70) cc_final: 0.8115 (t0) REVERT: A 4346 MET cc_start: 0.8760 (mmt) cc_final: 0.8275 (mmt) REVERT: A 4348 MET cc_start: 0.8114 (mtm) cc_final: 0.7554 (ptm) REVERT: A 4386 ASN cc_start: 0.9120 (m-40) cc_final: 0.8877 (m-40) REVERT: A 4419 MET cc_start: 0.5311 (ppp) cc_final: 0.4855 (ppp) REVERT: A 4537 GLU cc_start: 0.6681 (tp30) cc_final: 0.6466 (tp30) outliers start: 48 outliers final: 33 residues processed: 270 average time/residue: 0.1467 time to fit residues: 66.5572 Evaluate side-chains 267 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2369 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 3031 THR Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 295 optimal weight: 40.0000 chunk 78 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3155 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 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 = 0.4400 r_free = 0.4400 target = 0.159495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.118761 restraints weight = 50692.386| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.39 r_work: 0.3690 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25086 Z= 0.125 Angle : 0.527 10.995 34123 Z= 0.261 Chirality : 0.040 0.247 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.093 86.419 3575 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.60 % Allowed : 15.37 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 3235 helix: 1.87 (0.13), residues: 1680 sheet: -0.74 (0.30), residues: 314 loop : -0.43 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2863 TYR 0.023 0.001 TYR A2496 PHE 0.054 0.001 PHE A4413 TRP 0.048 0.001 TRP A2500 HIS 0.004 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00286 (25086) covalent geometry : angle 0.52713 (34123) hydrogen bonds : bond 0.03597 ( 1369) hydrogen bonds : angle 4.25631 ( 4038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1658 PHE cc_start: 0.6174 (m-80) cc_final: 0.5506 (m-10) REVERT: A 1677 SER cc_start: 0.8284 (m) cc_final: 0.7996 (t) REVERT: A 2045 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 2372 ASP cc_start: 0.7914 (p0) cc_final: 0.7140 (m-30) REVERT: A 2606 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7487 (t80) REVERT: A 2770 THR cc_start: 0.8400 (m) cc_final: 0.8003 (p) REVERT: A 2995 ASP cc_start: 0.8411 (m-30) cc_final: 0.8079 (t70) REVERT: A 3043 MET cc_start: 0.7285 (mmp) cc_final: 0.6803 (tpp) REVERT: A 3164 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6344 (mtp180) REVERT: A 3195 GLU cc_start: 0.7352 (tp30) cc_final: 0.6945 (tp30) REVERT: A 3199 MET cc_start: 0.5791 (tmm) cc_final: 0.5513 (tmm) REVERT: A 3586 TYR cc_start: 0.7763 (m-80) cc_final: 0.7383 (m-80) REVERT: A 3641 TYR cc_start: 0.7870 (p90) cc_final: 0.7468 (p90) REVERT: A 3677 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7925 (mm) REVERT: A 3791 MET cc_start: 0.5387 (mmt) cc_final: 0.3908 (tmm) REVERT: A 4098 ASN cc_start: 0.8740 (p0) cc_final: 0.8346 (p0) REVERT: A 4129 GLU cc_start: 0.8255 (mp0) cc_final: 0.7955 (mp0) REVERT: A 4217 ASP cc_start: 0.8355 (t70) cc_final: 0.8096 (t0) REVERT: A 4223 LEU cc_start: 0.8401 (mt) cc_final: 0.7717 (mt) REVERT: A 4346 MET cc_start: 0.8770 (mmt) cc_final: 0.8276 (mmt) REVERT: A 4348 MET cc_start: 0.8083 (mtm) cc_final: 0.7549 (ptm) REVERT: A 4386 ASN cc_start: 0.9131 (m-40) cc_final: 0.8909 (m-40) REVERT: A 4419 MET cc_start: 0.5293 (ppp) cc_final: 0.4934 (ppp) REVERT: A 4455 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 4537 GLU cc_start: 0.6660 (tp30) cc_final: 0.6455 (tp30) outliers start: 39 outliers final: 29 residues processed: 264 average time/residue: 0.1467 time to fit residues: 64.9315 Evaluate side-chains 266 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 3031 THR Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 185 optimal weight: 0.0040 chunk 281 optimal weight: 0.0170 chunk 315 optimal weight: 50.0000 chunk 251 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 323 optimal weight: 40.0000 chunk 276 optimal weight: 0.8980 overall best weight: 1.1432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.159347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118656 restraints weight = 50626.386| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.38 r_work: 0.3690 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25086 Z= 0.124 Angle : 0.529 8.862 34123 Z= 0.263 Chirality : 0.040 0.226 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.091 85.008 3575 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 15.49 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3235 helix: 1.87 (0.13), residues: 1680 sheet: -0.75 (0.30), residues: 313 loop : -0.40 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2863 TYR 0.022 0.001 TYR A2496 PHE 0.055 0.001 PHE A4413 TRP 0.035 0.001 TRP A2500 HIS 0.010 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00282 (25086) covalent geometry : angle 0.52903 (34123) hydrogen bonds : bond 0.03589 ( 1369) hydrogen bonds : angle 4.24398 ( 4038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1658 PHE cc_start: 0.6213 (m-80) cc_final: 0.5386 (m-10) REVERT: A 1677 SER cc_start: 0.8382 (m) cc_final: 0.8104 (t) REVERT: A 1766 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 2045 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 2606 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 2770 THR cc_start: 0.8409 (m) cc_final: 0.8018 (p) REVERT: A 2995 ASP cc_start: 0.8412 (m-30) cc_final: 0.8165 (t70) REVERT: A 2999 VAL cc_start: 0.8553 (t) cc_final: 0.8232 (p) REVERT: A 3043 MET cc_start: 0.7269 (mmp) cc_final: 0.6785 (tpp) REVERT: A 3068 MET cc_start: 0.7573 (ppp) cc_final: 0.7153 (ppp) REVERT: A 3164 ARG cc_start: 0.6891 (mtt180) cc_final: 0.6355 (mtp180) REVERT: A 3195 GLU cc_start: 0.7343 (tp30) cc_final: 0.6928 (tp30) REVERT: A 3199 MET cc_start: 0.5838 (tmm) cc_final: 0.5555 (tmm) REVERT: A 3586 TYR cc_start: 0.7779 (m-80) cc_final: 0.7433 (m-80) REVERT: A 3641 TYR cc_start: 0.7904 (p90) cc_final: 0.7514 (t80) REVERT: A 3677 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7957 (mm) REVERT: A 3791 MET cc_start: 0.5460 (mmt) cc_final: 0.4014 (tmm) REVERT: A 4098 ASN cc_start: 0.8740 (p0) cc_final: 0.8338 (p0) REVERT: A 4129 GLU cc_start: 0.8244 (mp0) cc_final: 0.7959 (mp0) REVERT: A 4217 ASP cc_start: 0.8378 (t70) cc_final: 0.8111 (t0) REVERT: A 4223 LEU cc_start: 0.8401 (mt) cc_final: 0.7708 (mt) REVERT: A 4348 MET cc_start: 0.8070 (mtm) cc_final: 0.7556 (ptm) REVERT: A 4386 ASN cc_start: 0.9093 (m-40) cc_final: 0.8857 (m-40) REVERT: A 4419 MET cc_start: 0.5422 (ppp) cc_final: 0.5144 (ppp) REVERT: A 4455 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 4552 THR cc_start: 0.8206 (p) cc_final: 0.7961 (t) outliers start: 47 outliers final: 32 residues processed: 274 average time/residue: 0.1571 time to fit residues: 71.8748 Evaluate side-chains 278 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3031 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 121 optimal weight: 0.0870 chunk 166 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 50.0000 chunk 302 optimal weight: 50.0000 chunk 301 optimal weight: 50.0000 chunk 154 optimal weight: 0.0270 chunk 240 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 298 optimal weight: 50.0000 overall best weight: 1.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3047 HIS A3155 HIS ** A4573 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 = 0.4383 r_free = 0.4383 target = 0.158227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.117686 restraints weight = 50364.106| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.35 r_work: 0.3676 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25086 Z= 0.145 Angle : 0.550 9.468 34123 Z= 0.273 Chirality : 0.041 0.208 3917 Planarity : 0.004 0.054 4441 Dihedral : 6.139 86.263 3575 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.93 % Allowed : 15.78 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3235 helix: 1.83 (0.13), residues: 1680 sheet: -0.75 (0.30), residues: 314 loop : -0.43 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2863 TYR 0.017 0.001 TYR A2496 PHE 0.019 0.002 PHE A3629 TRP 0.036 0.002 TRP A2845 HIS 0.004 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00333 (25086) covalent geometry : angle 0.54954 (34123) hydrogen bonds : bond 0.03673 ( 1369) hydrogen bonds : angle 4.26251 ( 4038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5887 (tpt) cc_final: 0.4996 (tmm) REVERT: A 1658 PHE cc_start: 0.6257 (m-80) cc_final: 0.5615 (m-80) REVERT: A 1677 SER cc_start: 0.8426 (m) cc_final: 0.8159 (t) REVERT: A 1679 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8056 (mtp-110) REVERT: A 1766 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 2045 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7791 (t0) REVERT: A 2606 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7543 (t80) REVERT: A 2770 THR cc_start: 0.8423 (m) cc_final: 0.8039 (p) REVERT: A 2995 ASP cc_start: 0.8391 (m-30) cc_final: 0.8152 (t70) REVERT: A 2999 VAL cc_start: 0.8560 (t) cc_final: 0.8249 (p) REVERT: A 3008 MET cc_start: 0.8198 (pmm) cc_final: 0.7915 (pmm) REVERT: A 3043 MET cc_start: 0.7235 (mmp) cc_final: 0.6746 (tpp) REVERT: A 3068 MET cc_start: 0.7706 (ppp) cc_final: 0.7263 (ppp) REVERT: A 3164 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6359 (mtp180) REVERT: A 3195 GLU cc_start: 0.7351 (tp30) cc_final: 0.6927 (tp30) REVERT: A 3199 MET cc_start: 0.5866 (tmm) cc_final: 0.5560 (tmm) REVERT: A 3586 TYR cc_start: 0.7833 (m-80) cc_final: 0.7498 (m-80) REVERT: A 3641 TYR cc_start: 0.7928 (p90) cc_final: 0.7638 (t80) REVERT: A 3677 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 3791 MET cc_start: 0.5385 (mmt) cc_final: 0.3934 (tmm) REVERT: A 4098 ASN cc_start: 0.8775 (p0) cc_final: 0.8352 (p0) REVERT: A 4129 GLU cc_start: 0.8273 (mp0) cc_final: 0.7974 (mp0) REVERT: A 4217 ASP cc_start: 0.8384 (t70) cc_final: 0.8122 (t0) REVERT: A 4348 MET cc_start: 0.8174 (mtm) cc_final: 0.7561 (ptm) REVERT: A 4386 ASN cc_start: 0.9141 (m-40) cc_final: 0.8936 (m-40) REVERT: A 4455 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 4552 THR cc_start: 0.8083 (p) cc_final: 0.7867 (t) outliers start: 47 outliers final: 36 residues processed: 277 average time/residue: 0.1616 time to fit residues: 73.9935 Evaluate side-chains 286 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1842 MET Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2369 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 185 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 217 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 250 optimal weight: 0.3980 chunk 299 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 214 optimal weight: 0.0060 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 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 = 0.4409 r_free = 0.4409 target = 0.160307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.120095 restraints weight = 50362.817| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.37 r_work: 0.3714 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25086 Z= 0.101 Angle : 0.533 10.394 34123 Z= 0.261 Chirality : 0.041 0.341 3917 Planarity : 0.003 0.053 4441 Dihedral : 6.029 80.076 3575 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.27 % Allowed : 16.76 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3235 helix: 1.91 (0.13), residues: 1676 sheet: -0.73 (0.30), residues: 315 loop : -0.39 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2863 TYR 0.018 0.001 TYR A2496 PHE 0.036 0.001 PHE A4413 TRP 0.039 0.001 TRP A2845 HIS 0.012 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00218 (25086) covalent geometry : angle 0.53325 (34123) hydrogen bonds : bond 0.03479 ( 1369) hydrogen bonds : angle 4.18860 ( 4038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5765 (tpt) cc_final: 0.4863 (tmm) REVERT: A 1658 PHE cc_start: 0.6211 (m-80) cc_final: 0.5648 (m-80) REVERT: A 1677 SER cc_start: 0.8480 (m) cc_final: 0.8214 (t) REVERT: A 1766 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 2045 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7741 (t0) REVERT: A 2606 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 2770 THR cc_start: 0.8372 (m) cc_final: 0.7969 (p) REVERT: A 2863 ARG cc_start: 0.7631 (tpt90) cc_final: 0.7130 (tpt90) REVERT: A 2995 ASP cc_start: 0.8340 (m-30) cc_final: 0.8134 (t70) REVERT: A 2999 VAL cc_start: 0.8530 (t) cc_final: 0.8230 (p) REVERT: A 3068 MET cc_start: 0.7632 (ppp) cc_final: 0.7229 (ppp) REVERT: A 3164 ARG cc_start: 0.6831 (mtt180) cc_final: 0.6327 (mtp180) REVERT: A 3195 GLU cc_start: 0.7325 (tp30) cc_final: 0.6898 (tp30) REVERT: A 3199 MET cc_start: 0.5853 (tmm) cc_final: 0.5566 (tmm) REVERT: A 3586 TYR cc_start: 0.7748 (m-80) cc_final: 0.7475 (m-80) REVERT: A 3641 TYR cc_start: 0.7910 (p90) cc_final: 0.7655 (t80) REVERT: A 3677 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 3694 SER cc_start: 0.8646 (t) cc_final: 0.8113 (p) REVERT: A 3700 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7738 (m110) REVERT: A 3791 MET cc_start: 0.5451 (mmt) cc_final: 0.4008 (tmm) REVERT: A 4098 ASN cc_start: 0.8707 (p0) cc_final: 0.8367 (p0) REVERT: A 4129 GLU cc_start: 0.8227 (mp0) cc_final: 0.7935 (mp0) REVERT: A 4217 ASP cc_start: 0.8349 (t70) cc_final: 0.8082 (t0) REVERT: A 4348 MET cc_start: 0.8075 (mtm) cc_final: 0.7581 (ptm) REVERT: A 4386 ASN cc_start: 0.9082 (m-40) cc_final: 0.8868 (m-40) REVERT: A 4455 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (mt) REVERT: A 4552 THR cc_start: 0.8077 (p) cc_final: 0.7860 (t) outliers start: 31 outliers final: 22 residues processed: 278 average time/residue: 0.1580 time to fit residues: 73.3373 Evaluate side-chains 277 residues out of total 2881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3700 ASN Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 297 optimal weight: 50.0000 chunk 294 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 249 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 282 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN A3047 HIS ** A4573 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 = 0.4331 r_free = 0.4331 target = 0.154152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113269 restraints weight = 50777.079| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.32 r_work: 0.3595 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25086 Z= 0.291 Angle : 0.697 12.407 34123 Z= 0.351 Chirality : 0.045 0.296 3917 Planarity : 0.005 0.068 4441 Dihedral : 6.627 83.994 3575 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.44 % Allowed : 17.09 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3235 helix: 1.50 (0.13), residues: 1677 sheet: -1.08 (0.28), residues: 344 loop : -0.62 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2863 TYR 0.026 0.002 TYR A2496 PHE 0.029 0.003 PHE A2165 TRP 0.051 0.002 TRP A2500 HIS 0.007 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00673 (25086) covalent geometry : angle 0.69723 (34123) hydrogen bonds : bond 0.04506 ( 1369) hydrogen bonds : angle 4.60311 ( 4038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7113.94 seconds wall clock time: 122 minutes 13.01 seconds (7333.01 seconds total)