Starting phenix.real_space_refine on Thu Sep 18 23:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.map" model { file = "/net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dju_46938/09_2025/9dju_46938.cif" } resolution = 4.0 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 97 5.16 5 C 13233 2.51 5 N 3472 2.21 5 O 3845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s 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: 20656 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2317, 18011 Classifications: {'peptide': 2317} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'PTRANS': 60, 'TRANS': 2256} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 968 Unresolved non-hydrogen dihedrals: 642 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'ASN:plan1': 13, 'ARG:plan': 12, 'GLU:plan': 36, 'GLN:plan1': 8, 'HIS:plan': 3, 'ASP:plan': 20, 'TRP:plan': 3, 'PHE:plan': 9, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 452 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2533 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 310} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.06, per 1000 atoms: 0.24 Number of scatterers: 20656 At special positions: 0 Unit cell: (109.04, 149.64, 175.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 9 15.00 O 3845 8.00 N 3472 7.00 C 13233 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5036 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 22 sheets defined 56.4% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 1370 through 1380 Processing helix chain 'A' and resid 1397 through 1406 removed outlier: 3.710A pdb=" N LEU A1401 " --> pdb=" O GLU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1458 removed outlier: 4.270A pdb=" N ASP A1454 " --> pdb=" O PHE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1462 removed outlier: 3.808A pdb=" N ASN A1462 " --> pdb=" O LEU A1459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1459 through 1462' Processing helix chain 'A' and resid 1474 through 1492 Processing helix chain 'A' and resid 1506 through 1534 Processing helix chain 'A' and resid 1535 through 1540 removed outlier: 3.568A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.881A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.744A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.631A pdb=" N ASN A1717 " --> pdb=" O GLY A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1730 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.797A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1814 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.765A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1853 removed outlier: 3.559A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1915 removed outlier: 3.731A pdb=" N SER A1915 " --> pdb=" O ASN A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.539A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1970 through 1988 removed outlier: 4.343A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 4.176A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2002 removed outlier: 3.934A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2008 through 2022 Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 removed outlier: 3.840A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2146 removed outlier: 3.514A pdb=" N LYS A2146 " --> pdb=" O GLY A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2143 through 2146' Processing helix chain 'A' and resid 2160 through 2165 removed outlier: 4.408A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2205 through 2210 Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.629A pdb=" N LYS A2225 " --> pdb=" O SER A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.118A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2299 Processing helix chain 'A' and resid 2300 through 2305 removed outlier: 5.384A pdb=" N GLN A2303 " --> pdb=" O GLN A2300 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A2304 " --> pdb=" O TRP A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2345 Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.841A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.526A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2460 removed outlier: 3.676A pdb=" N LEU A2455 " --> pdb=" O THR A2451 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2513 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.811A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 3.586A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A2586 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2582 through 2587' Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.663A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A2607 " --> pdb=" O CYS A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.966A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2656 Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.979A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2778 Processing helix chain 'A' and resid 2791 through 2810 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 4.205A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2860 Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2899 through 2905 Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2934 through 2936 No H-bonds generated for 'chain 'A' and resid 2934 through 2936' Processing helix chain 'A' and resid 2961 through 2980 Processing helix chain 'A' and resid 2989 through 3025 Processing helix chain 'A' and resid 3299 through 3334 removed outlier: 4.836A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A3323 " --> pdb=" O GLU A3319 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A3334 " --> pdb=" O TYR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3357 Processing helix chain 'A' and resid 3366 through 3371 Processing helix chain 'A' and resid 3372 through 3381 Processing helix chain 'A' and resid 3387 through 3400 Processing helix chain 'A' and resid 3413 through 3423 Processing helix chain 'A' and resid 3436 through 3447 Processing helix chain 'A' and resid 3454 through 3458 Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3513 removed outlier: 3.671A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3537 Processing helix chain 'A' and resid 3539 through 3572 Processing helix chain 'A' and resid 3583 through 3604 Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.819A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3635 Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.643A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A3659 " --> pdb=" O ARG A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3710 Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.634A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3756 through 3768 Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3808 removed outlier: 3.757A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3835 Processing helix chain 'A' and resid 3843 through 3846 removed outlier: 3.573A pdb=" N MET A3846 " --> pdb=" O ASN A3843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3843 through 3846' Processing helix chain 'A' and resid 3847 through 3860 removed outlier: 4.013A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3890 Processing helix chain 'A' and resid 3902 through 3914 Processing helix chain 'A' and resid 3923 through 3945 removed outlier: 3.813A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A3945 " --> pdb=" O ALA A3941 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.769A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A3975 " --> pdb=" O VAL A3971 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 4.184A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4089 Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1571 through 1575 removed outlier: 3.716A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A1575 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.817A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1821 Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.423A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA7, first strand: chain 'A' and resid 2441 through 2444 removed outlier: 3.615A pdb=" N VAL A2441 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A2487 " --> pdb=" O ILE A2443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AA9, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.537A pdb=" N SER A2697 " --> pdb=" O LYS A2705 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.606A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET A2756 " --> pdb=" O VAL A2887 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A2889 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 3.840A pdb=" N GLN A3453 " --> pdb=" O LEU A3429 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A3496 " --> pdb=" O PRO A3405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 3.575A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A3786 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N CYS A3877 " --> pdb=" O PHE A3786 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N MET A3788 " --> pdb=" O CYS A3877 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 3.575A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A3786 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.505A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.389A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 463 " --> pdb=" O GLY C 483 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 163 removed outlier: 4.470A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.909A pdb=" N ASP C 205 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 223 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRP C 236 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C 222 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 256 through 260 Processing sheet with id=AC1, first strand: chain 'C' and resid 279 through 282 Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.888A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 340 through 346 removed outlier: 4.370A pdb=" N TYR C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE C 382 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR C 412 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE C 384 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 410 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 420 through 426 removed outlier: 4.036A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 426 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1167 hydrogen bonds defined for protein. 3432 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: 5.76 Time building geometry restraints manager: 2.49 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: 6414 1.34 - 1.46: 3680 1.46 - 1.58: 10815 1.58 - 1.70: 14 1.70 - 1.82: 149 Bond restraints: 21072 Sorted by residual: bond pdb=" CG1 ILE A3529 " pdb=" CD1 ILE A3529 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.35e+00 bond pdb=" CG MET A2925 " pdb=" SD MET A2925 " ideal model delta sigma weight residual 1.803 1.766 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" C MET A3541 " pdb=" O MET A3541 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.35e-02 5.49e+03 1.78e+00 bond pdb=" CG1 ILE A2226 " pdb=" CD1 ILE A2226 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" CA GLU A1576 " pdb=" CB GLU A1576 " ideal model delta sigma weight residual 1.527 1.548 -0.020 1.70e-02 3.46e+03 1.45e+00 ... (remaining 21067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 27834 1.94 - 3.89: 586 3.89 - 5.83: 112 5.83 - 7.77: 35 7.77 - 9.72: 8 Bond angle restraints: 28575 Sorted by residual: angle pdb=" C ASN A3393 " pdb=" N MET A3394 " pdb=" CA MET A3394 " ideal model delta sigma weight residual 121.14 114.72 6.42 1.75e+00 3.27e-01 1.34e+01 angle pdb=" N GLN A2059 " pdb=" CA GLN A2059 " pdb=" CB GLN A2059 " ideal model delta sigma weight residual 110.16 115.39 -5.23 1.48e+00 4.57e-01 1.25e+01 angle pdb=" C PHE A2972 " pdb=" N ASP A2973 " pdb=" CA ASP A2973 " ideal model delta sigma weight residual 121.14 115.11 6.03 1.75e+00 3.27e-01 1.19e+01 angle pdb=" N GLU A2602 " pdb=" CA GLU A2602 " pdb=" CB GLU A2602 " ideal model delta sigma weight residual 110.40 115.87 -5.47 1.63e+00 3.76e-01 1.13e+01 angle pdb=" N GLY A2846 " pdb=" CA GLY A2846 " pdb=" C GLY A2846 " ideal model delta sigma weight residual 111.47 117.18 -5.71 1.72e+00 3.38e-01 1.10e+01 ... (remaining 28570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 11477 21.25 - 42.49: 965 42.49 - 63.74: 70 63.74 - 84.99: 27 84.99 - 106.23: 5 Dihedral angle restraints: 12544 sinusoidal: 4815 harmonic: 7729 Sorted by residual: dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 -162.22 -106.23 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" CA PRO A2731 " pdb=" C PRO A2731 " pdb=" N MET A2732 " pdb=" CA MET A2732 " ideal model delta harmonic sigma weight residual -180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA MET A2049 " pdb=" C MET A2049 " pdb=" N SER A2050 " pdb=" CA SER A2050 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 12541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2759 0.061 - 0.121: 492 0.121 - 0.182: 46 0.182 - 0.243: 4 0.243 - 0.304: 2 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CB ILE A2395 " pdb=" CA ILE A2395 " pdb=" CG1 ILE A2395 " pdb=" CG2 ILE A2395 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A1765 " pdb=" CA ILE A1765 " pdb=" CG1 ILE A1765 " pdb=" CG2 ILE A1765 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE A3814 " pdb=" CA ILE A3814 " pdb=" CG1 ILE A3814 " pdb=" CG2 ILE A3814 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3300 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2992 " 0.032 2.00e-02 2.50e+03 2.13e-02 7.92e+00 pdb=" CG PHE A2992 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A2992 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A2992 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A2992 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A2992 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A2992 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A2392 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A2393 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A2393 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A2393 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A2973 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" CG ASP A2973 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A2973 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A2973 " 0.014 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1940 2.75 - 3.28: 20891 3.28 - 3.82: 35727 3.82 - 4.36: 38329 4.36 - 4.90: 65766 Nonbonded interactions: 162653 Sorted by model distance: nonbonded pdb=" O SER C 274 " pdb=" NE1 TRP C 299 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR C 202 " pdb=" O SER C 257 " model vdw 2.210 3.040 nonbonded pdb=" O TYR A3683 " pdb=" OG SER A3687 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A2458 " pdb=" OG1 THR A2462 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A1800 " pdb=" O MET A1921 " model vdw 2.246 3.040 ... (remaining 162648 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.020 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 0.060 21072 Z= 0.142 Angle : 0.711 9.716 28575 Z= 0.356 Chirality : 0.046 0.304 3303 Planarity : 0.005 0.070 3576 Dihedral : 14.719 106.233 7508 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.16), residues: 2581 helix: 0.49 (0.14), residues: 1381 sheet: 0.04 (0.31), residues: 295 loop : -1.50 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A3543 TYR 0.026 0.001 TYR A2849 PHE 0.042 0.002 PHE A2992 TRP 0.018 0.001 TRP A3379 HIS 0.007 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00295 (21072) covalent geometry : angle 0.71073 (28575) hydrogen bonds : bond 0.12279 ( 1164) hydrogen bonds : angle 6.02686 ( 3432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1913 LYS cc_start: 0.9081 (tttt) cc_final: 0.8573 (mtpp) REVERT: A 1984 VAL cc_start: 0.7646 (t) cc_final: 0.7398 (t) REVERT: A 2171 ASP cc_start: 0.6227 (t70) cc_final: 0.5586 (t70) REVERT: A 2201 HIS cc_start: 0.6602 (m170) cc_final: 0.6221 (m170) REVERT: A 2282 ASN cc_start: 0.8538 (m-40) cc_final: 0.8302 (m110) REVERT: A 2402 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7327 (tptp) REVERT: A 2971 HIS cc_start: 0.8035 (m90) cc_final: 0.7359 (m-70) REVERT: A 2975 ASN cc_start: 0.8919 (m110) cc_final: 0.8535 (m110) REVERT: A 3413 HIS cc_start: 0.8351 (m90) cc_final: 0.7817 (m-70) REVERT: A 3500 ASP cc_start: 0.8104 (t0) cc_final: 0.7672 (p0) REVERT: A 3544 LYS cc_start: 0.8100 (tppt) cc_final: 0.7529 (tttt) REVERT: A 3717 GLU cc_start: 0.9029 (tp30) cc_final: 0.8478 (pt0) REVERT: A 3748 TRP cc_start: 0.8226 (t-100) cc_final: 0.7941 (t-100) REVERT: A 3943 THR cc_start: 0.6972 (m) cc_final: 0.6766 (m) REVERT: C 145 ARG cc_start: 0.8819 (ptp-110) cc_final: 0.8066 (mmp-170) REVERT: C 146 ASN cc_start: 0.9138 (p0) cc_final: 0.8578 (p0) REVERT: C 324 TRP cc_start: 0.7654 (m-10) cc_final: 0.7299 (t60) REVERT: C 344 LYS cc_start: 0.6429 (tppt) cc_final: 0.6172 (ttpt) REVERT: C 426 ARG cc_start: 0.7674 (ptt180) cc_final: 0.6113 (ttp80) REVERT: C 448 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 490 ASN cc_start: 0.7221 (m-40) cc_final: 0.6947 (m-40) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1606 time to fit residues: 83.0982 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1444 ASN A1492 GLN A1717 ASN A1864 ASN ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3472 HIS A3845 GLN ** A3856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.107428 restraints weight = 56657.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107950 restraints weight = 39410.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109432 restraints weight = 28138.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.109903 restraints weight = 21244.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110127 restraints weight = 18819.324| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 21072 Z= 0.280 Angle : 0.757 8.372 28575 Z= 0.393 Chirality : 0.046 0.189 3303 Planarity : 0.005 0.083 3576 Dihedral : 6.136 118.723 2861 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.20 % Allowed : 12.48 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.16), residues: 2581 helix: 0.66 (0.14), residues: 1399 sheet: -0.52 (0.29), residues: 307 loop : -1.51 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1815 TYR 0.023 0.002 TYR A2615 PHE 0.072 0.003 PHE A2992 TRP 0.018 0.002 TRP A2084 HIS 0.014 0.002 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00632 (21072) covalent geometry : angle 0.75670 (28575) hydrogen bonds : bond 0.04765 ( 1164) hydrogen bonds : angle 5.19985 ( 3432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1485 MET cc_start: 0.8381 (mtt) cc_final: 0.7553 (mmm) REVERT: A 1879 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 2118 MET cc_start: 0.7822 (tpp) cc_final: 0.7541 (tpp) REVERT: A 2171 ASP cc_start: 0.6967 (t70) cc_final: 0.6049 (t70) REVERT: A 2200 ASP cc_start: 0.7862 (p0) cc_final: 0.7296 (p0) REVERT: A 2201 HIS cc_start: 0.6778 (m170) cc_final: 0.6372 (m90) REVERT: A 2270 ASN cc_start: 0.8163 (t0) cc_final: 0.7489 (p0) REVERT: A 2282 ASN cc_start: 0.8347 (m-40) cc_final: 0.8068 (m110) REVERT: A 2444 ASN cc_start: 0.8216 (t0) cc_final: 0.7919 (t0) REVERT: A 2558 TYR cc_start: 0.8102 (t80) cc_final: 0.7484 (t80) REVERT: A 2680 TYR cc_start: 0.7209 (m-80) cc_final: 0.6393 (m-10) REVERT: A 2732 MET cc_start: 0.6821 (tpp) cc_final: 0.6125 (tpp) REVERT: A 2844 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.5380 (m-80) REVERT: A 2975 ASN cc_start: 0.8915 (m110) cc_final: 0.8613 (m110) REVERT: A 3413 HIS cc_start: 0.8408 (m90) cc_final: 0.7914 (m-70) REVERT: A 3472 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6213 (t-90) REVERT: A 3500 ASP cc_start: 0.8288 (t0) cc_final: 0.7724 (p0) REVERT: A 3595 MET cc_start: 0.6679 (ppp) cc_final: 0.6457 (ptt) REVERT: A 3616 GLU cc_start: 0.7528 (pp20) cc_final: 0.7239 (pp20) REVERT: A 3717 GLU cc_start: 0.8995 (tp30) cc_final: 0.8434 (pt0) REVERT: A 3748 TRP cc_start: 0.8236 (t-100) cc_final: 0.7996 (t-100) REVERT: A 3934 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7065 (t60) REVERT: A 4079 LYS cc_start: 0.8778 (tptt) cc_final: 0.8237 (ttmt) REVERT: C 145 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8114 (mmp-170) REVERT: C 146 ASN cc_start: 0.9124 (p0) cc_final: 0.8520 (p0) REVERT: C 324 TRP cc_start: 0.7609 (m-10) cc_final: 0.7318 (t60) REVERT: C 344 LYS cc_start: 0.6390 (tppt) cc_final: 0.5999 (ttpt) REVERT: C 374 VAL cc_start: 0.7077 (p) cc_final: 0.6671 (p) REVERT: C 385 TRP cc_start: 0.6538 (m100) cc_final: 0.5330 (m100) REVERT: C 426 ARG cc_start: 0.7507 (ptt180) cc_final: 0.6188 (ttp80) REVERT: C 490 ASN cc_start: 0.7121 (m-40) cc_final: 0.6811 (m-40) outliers start: 48 outliers final: 31 residues processed: 315 average time/residue: 0.1350 time to fit residues: 67.6337 Evaluate side-chains 279 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2063 MET Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2313 VAL Chi-restraints excluded: chain A residue 2366 LEU Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2770 THR Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 3379 TRP Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1492 GLN A1714 GLN ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2180 ASN ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3472 HIS ** A3856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 457 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.142074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110595 restraints weight = 55903.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111278 restraints weight = 34597.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112432 restraints weight = 23790.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112707 restraints weight = 20557.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.112936 restraints weight = 17880.846| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21072 Z= 0.169 Angle : 0.628 10.010 28575 Z= 0.323 Chirality : 0.042 0.191 3303 Planarity : 0.004 0.071 3576 Dihedral : 5.995 117.107 2861 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.48 % Allowed : 16.65 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.16), residues: 2581 helix: 0.99 (0.14), residues: 1385 sheet: -0.59 (0.28), residues: 322 loop : -1.42 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2654 TYR 0.017 0.001 TYR C 180 PHE 0.044 0.002 PHE A2992 TRP 0.016 0.001 TRP A2084 HIS 0.007 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00384 (21072) covalent geometry : angle 0.62816 (28575) hydrogen bonds : bond 0.04141 ( 1164) hydrogen bonds : angle 4.85845 ( 3432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1828 TYR cc_start: 0.7759 (t80) cc_final: 0.7508 (t80) REVERT: A 1879 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8208 (mm) REVERT: A 2059 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: A 2158 LEU cc_start: 0.8463 (tp) cc_final: 0.7871 (tp) REVERT: A 2171 ASP cc_start: 0.6961 (t70) cc_final: 0.6034 (t70) REVERT: A 2200 ASP cc_start: 0.7800 (p0) cc_final: 0.7379 (p0) REVERT: A 2201 HIS cc_start: 0.6616 (m170) cc_final: 0.6223 (m90) REVERT: A 2270 ASN cc_start: 0.8130 (t0) cc_final: 0.7442 (p0) REVERT: A 2282 ASN cc_start: 0.8301 (m-40) cc_final: 0.7993 (m110) REVERT: A 2300 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: A 2312 ASP cc_start: 0.5805 (m-30) cc_final: 0.5602 (m-30) REVERT: A 2444 ASN cc_start: 0.8123 (t0) cc_final: 0.7914 (t0) REVERT: A 2574 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: A 2680 TYR cc_start: 0.7171 (m-80) cc_final: 0.6332 (m-10) REVERT: A 2844 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5298 (m-80) REVERT: A 2975 ASN cc_start: 0.8901 (m110) cc_final: 0.8581 (m110) REVERT: A 3413 HIS cc_start: 0.8295 (m90) cc_final: 0.7905 (m-70) REVERT: A 3472 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6345 (t-90) REVERT: A 3500 ASP cc_start: 0.8237 (t0) cc_final: 0.7682 (p0) REVERT: A 3595 MET cc_start: 0.6722 (ppp) cc_final: 0.6506 (ptt) REVERT: A 3717 GLU cc_start: 0.8984 (tp30) cc_final: 0.8438 (pt0) REVERT: C 145 ARG cc_start: 0.8826 (ptp-110) cc_final: 0.8179 (mmp-170) REVERT: C 146 ASN cc_start: 0.9109 (p0) cc_final: 0.8479 (p0) REVERT: C 191 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7801 (pp) REVERT: C 195 GLN cc_start: 0.7068 (tm-30) cc_final: 0.5914 (mt0) REVERT: C 204 MET cc_start: 0.7119 (ppp) cc_final: 0.6827 (ppp) REVERT: C 344 LYS cc_start: 0.6500 (tppt) cc_final: 0.6078 (ttpt) REVERT: C 374 VAL cc_start: 0.7201 (p) cc_final: 0.6951 (p) REVERT: C 385 TRP cc_start: 0.6713 (m100) cc_final: 0.5454 (m100) REVERT: C 426 ARG cc_start: 0.7397 (ptt180) cc_final: 0.6068 (ttp80) REVERT: C 490 ASN cc_start: 0.7031 (m-40) cc_final: 0.6765 (m-40) outliers start: 54 outliers final: 29 residues processed: 308 average time/residue: 0.1318 time to fit residues: 65.3854 Evaluate side-chains 289 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3813 ILE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 67 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 7 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 GLN A1714 GLN ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2300 GLN A4013 HIS C 294 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 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 = 0.4139 r_free = 0.4139 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111495 restraints weight = 58881.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110759 restraints weight = 38051.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112483 restraints weight = 29016.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.112789 restraints weight = 22423.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113153 restraints weight = 19574.149| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21072 Z= 0.179 Angle : 0.629 10.926 28575 Z= 0.322 Chirality : 0.043 0.167 3303 Planarity : 0.004 0.070 3576 Dihedral : 6.020 118.604 2861 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.44 % Allowed : 18.49 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.16), residues: 2581 helix: 1.10 (0.14), residues: 1374 sheet: -0.55 (0.28), residues: 321 loop : -1.43 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2654 TYR 0.015 0.001 TYR C 180 PHE 0.026 0.002 PHE A2302 TRP 0.017 0.001 TRP A2084 HIS 0.009 0.001 HIS A3472 Details of bonding type rmsd covalent geometry : bond 0.00404 (21072) covalent geometry : angle 0.62934 (28575) hydrogen bonds : bond 0.03975 ( 1164) hydrogen bonds : angle 4.77882 ( 3432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1786 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 1879 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 2059 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: A 2118 MET cc_start: 0.7740 (tpp) cc_final: 0.6660 (mtt) REVERT: A 2171 ASP cc_start: 0.7006 (t70) cc_final: 0.5972 (t70) REVERT: A 2201 HIS cc_start: 0.6573 (m170) cc_final: 0.6255 (m170) REVERT: A 2232 LYS cc_start: 0.9025 (tptp) cc_final: 0.8762 (tptm) REVERT: A 2270 ASN cc_start: 0.8170 (t0) cc_final: 0.7410 (p0) REVERT: A 2282 ASN cc_start: 0.8422 (m-40) cc_final: 0.8093 (m110) REVERT: A 2300 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: A 2444 ASN cc_start: 0.8071 (t0) cc_final: 0.7829 (t0) REVERT: A 2574 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: A 2621 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: A 2680 TYR cc_start: 0.7256 (m-80) cc_final: 0.6354 (m-10) REVERT: A 2844 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5373 (m-80) REVERT: A 2975 ASN cc_start: 0.8897 (m110) cc_final: 0.8601 (m110) REVERT: A 3413 HIS cc_start: 0.8392 (m90) cc_final: 0.7984 (m-70) REVERT: A 3421 TYR cc_start: 0.6778 (t80) cc_final: 0.6432 (t80) REVERT: A 3472 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6850 (t-170) REVERT: A 3500 ASP cc_start: 0.8274 (t0) cc_final: 0.7677 (p0) REVERT: A 3517 HIS cc_start: 0.7514 (t70) cc_final: 0.5993 (t-90) REVERT: A 3616 GLU cc_start: 0.7472 (pp20) cc_final: 0.7224 (pp20) REVERT: A 3717 GLU cc_start: 0.8984 (tp30) cc_final: 0.8397 (pt0) REVERT: A 4087 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8161 (mm-40) REVERT: C 145 ARG cc_start: 0.8881 (ptp-110) cc_final: 0.8283 (mmp-170) REVERT: C 146 ASN cc_start: 0.9076 (p0) cc_final: 0.8437 (p0) REVERT: C 195 GLN cc_start: 0.7148 (tm-30) cc_final: 0.5937 (mt0) REVERT: C 344 LYS cc_start: 0.6443 (tppt) cc_final: 0.6051 (ttpt) REVERT: C 374 VAL cc_start: 0.7217 (p) cc_final: 0.6974 (p) REVERT: C 385 TRP cc_start: 0.6549 (m100) cc_final: 0.5456 (m100) REVERT: C 426 ARG cc_start: 0.7513 (ptt180) cc_final: 0.6109 (ttp80) REVERT: C 448 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 450 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8032 (mm) REVERT: C 490 ASN cc_start: 0.7227 (m-40) cc_final: 0.6932 (m-40) outliers start: 75 outliers final: 49 residues processed: 315 average time/residue: 0.1453 time to fit residues: 72.9792 Evaluate side-chains 313 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2712 LEU Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3813 ILE Chi-restraints excluded: chain A residue 3844 ILE Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 256 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 HIS A3472 HIS C 277 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.144495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113825 restraints weight = 58218.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112894 restraints weight = 39204.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114510 restraints weight = 28571.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.115358 restraints weight = 21092.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.115522 restraints weight = 18360.755| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21072 Z= 0.125 Angle : 0.593 10.959 28575 Z= 0.301 Chirality : 0.042 0.166 3303 Planarity : 0.004 0.057 3576 Dihedral : 5.902 116.505 2861 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.89 % Allowed : 20.50 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.17), residues: 2581 helix: 1.27 (0.14), residues: 1371 sheet: -0.32 (0.29), residues: 306 loop : -1.29 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2830 TYR 0.021 0.001 TYR C 187 PHE 0.028 0.001 PHE A2302 TRP 0.018 0.001 TRP C 453 HIS 0.006 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00279 (21072) covalent geometry : angle 0.59343 (28575) hydrogen bonds : bond 0.03695 ( 1164) hydrogen bonds : angle 4.59581 ( 3432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1879 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 1913 LYS cc_start: 0.9080 (tttt) cc_final: 0.8562 (mtpp) REVERT: A 2059 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: A 2118 MET cc_start: 0.7965 (tpp) cc_final: 0.6899 (mtt) REVERT: A 2158 LEU cc_start: 0.8098 (tp) cc_final: 0.7746 (tp) REVERT: A 2171 ASP cc_start: 0.6930 (t70) cc_final: 0.5915 (t70) REVERT: A 2201 HIS cc_start: 0.6454 (m170) cc_final: 0.6208 (m170) REVERT: A 2282 ASN cc_start: 0.8486 (m-40) cc_final: 0.8175 (m110) REVERT: A 2444 ASN cc_start: 0.7892 (t0) cc_final: 0.7642 (t0) REVERT: A 2574 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: A 2654 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.6705 (mmp-170) REVERT: A 2680 TYR cc_start: 0.7213 (m-80) cc_final: 0.6556 (m-80) REVERT: A 2830 ARG cc_start: 0.8218 (mpt-90) cc_final: 0.7983 (mmt90) REVERT: A 2844 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5401 (m-80) REVERT: A 2975 ASN cc_start: 0.8854 (m110) cc_final: 0.8531 (m110) REVERT: A 2977 TYR cc_start: 0.6937 (t80) cc_final: 0.6556 (t80) REVERT: A 3413 HIS cc_start: 0.8321 (m90) cc_final: 0.7996 (m-70) REVERT: A 3500 ASP cc_start: 0.8220 (t0) cc_final: 0.7648 (p0) REVERT: A 3717 GLU cc_start: 0.9034 (tp30) cc_final: 0.8444 (pt0) REVERT: A 3980 ILE cc_start: 0.8827 (mm) cc_final: 0.8612 (mm) REVERT: A 4087 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 145 ARG cc_start: 0.8849 (ptp-110) cc_final: 0.8257 (mmp-170) REVERT: C 146 ASN cc_start: 0.9066 (p0) cc_final: 0.8558 (p0) REVERT: C 195 GLN cc_start: 0.7097 (tm-30) cc_final: 0.5876 (mt0) REVERT: C 344 LYS cc_start: 0.6435 (tppt) cc_final: 0.6049 (ttpt) REVERT: C 374 VAL cc_start: 0.7249 (p) cc_final: 0.7027 (p) REVERT: C 385 TRP cc_start: 0.6475 (m100) cc_final: 0.5404 (m100) REVERT: C 426 ARG cc_start: 0.7587 (ptt180) cc_final: 0.6000 (ttp80) REVERT: C 448 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 450 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 490 ASN cc_start: 0.7138 (m-40) cc_final: 0.6859 (m-40) outliers start: 63 outliers final: 40 residues processed: 312 average time/residue: 0.1451 time to fit residues: 72.1926 Evaluate side-chains 297 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2890 THR Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 208 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 222 optimal weight: 0.0870 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3472 HIS C 245 GLN C 277 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.143540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112673 restraints weight = 58451.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111981 restraints weight = 36416.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.113589 restraints weight = 28026.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113915 restraints weight = 21443.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114223 restraints weight = 19208.431| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21072 Z= 0.149 Angle : 0.614 12.927 28575 Z= 0.310 Chirality : 0.042 0.172 3303 Planarity : 0.004 0.058 3576 Dihedral : 5.906 117.617 2861 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.62 % Allowed : 21.42 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.17), residues: 2581 helix: 1.29 (0.14), residues: 1372 sheet: -0.38 (0.29), residues: 315 loop : -1.29 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2654 TYR 0.018 0.001 TYR C 187 PHE 0.027 0.001 PHE C 185 TRP 0.018 0.001 TRP C 453 HIS 0.016 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00341 (21072) covalent geometry : angle 0.61367 (28575) hydrogen bonds : bond 0.03712 ( 1164) hydrogen bonds : angle 4.59722 ( 3432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1608 LEU cc_start: 0.8224 (mt) cc_final: 0.7972 (mp) REVERT: A 1786 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 1867 GLN cc_start: 0.7635 (tp40) cc_final: 0.7304 (tp40) REVERT: A 1879 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 1913 LYS cc_start: 0.9089 (tttt) cc_final: 0.8551 (mtpp) REVERT: A 2059 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: A 2158 LEU cc_start: 0.8126 (tp) cc_final: 0.7752 (tp) REVERT: A 2171 ASP cc_start: 0.7038 (t70) cc_final: 0.5989 (t70) REVERT: A 2201 HIS cc_start: 0.6518 (m170) cc_final: 0.6266 (m170) REVERT: A 2232 LYS cc_start: 0.9025 (tptp) cc_final: 0.8757 (tptm) REVERT: A 2270 ASN cc_start: 0.8086 (t0) cc_final: 0.7446 (p0) REVERT: A 2282 ASN cc_start: 0.8476 (m-40) cc_final: 0.8227 (m110) REVERT: A 2444 ASN cc_start: 0.7696 (t0) cc_final: 0.7468 (t0) REVERT: A 2574 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: A 2680 TYR cc_start: 0.7225 (m-80) cc_final: 0.6488 (m-80) REVERT: A 2844 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: A 2975 ASN cc_start: 0.8812 (m110) cc_final: 0.8504 (m110) REVERT: A 2977 TYR cc_start: 0.7045 (t80) cc_final: 0.6646 (t80) REVERT: A 3413 HIS cc_start: 0.8388 (m90) cc_final: 0.8038 (m-70) REVERT: A 3500 ASP cc_start: 0.8288 (t0) cc_final: 0.7677 (p0) REVERT: A 3717 GLU cc_start: 0.9028 (tp30) cc_final: 0.8413 (pt0) REVERT: A 3980 ILE cc_start: 0.8838 (mm) cc_final: 0.8622 (mm) REVERT: A 4087 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8241 (mm-40) REVERT: C 145 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8268 (mmp-170) REVERT: C 146 ASN cc_start: 0.9071 (p0) cc_final: 0.8578 (p0) REVERT: C 195 GLN cc_start: 0.7101 (tm-30) cc_final: 0.5894 (mt0) REVERT: C 344 LYS cc_start: 0.6451 (tppt) cc_final: 0.5982 (mtpt) REVERT: C 385 TRP cc_start: 0.6399 (m100) cc_final: 0.5444 (m100) REVERT: C 426 ARG cc_start: 0.7665 (ptt180) cc_final: 0.6086 (ttp80) REVERT: C 450 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7924 (mm) REVERT: C 490 ASN cc_start: 0.7128 (m-40) cc_final: 0.6800 (m-40) outliers start: 79 outliers final: 51 residues processed: 317 average time/residue: 0.1433 time to fit residues: 73.1961 Evaluate side-chains 311 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2313 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2653 TRP Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2704 PHE Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3418 ILE Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 228 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1714 GLN ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2138 ASN C 277 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.143620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113315 restraints weight = 56149.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112473 restraints weight = 36573.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113975 restraints weight = 26313.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.114348 restraints weight = 21949.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.114485 restraints weight = 19475.090| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21072 Z= 0.150 Angle : 0.627 11.960 28575 Z= 0.315 Chirality : 0.042 0.181 3303 Planarity : 0.004 0.055 3576 Dihedral : 5.940 117.962 2861 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.85 % Allowed : 22.06 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.17), residues: 2581 helix: 1.32 (0.14), residues: 1373 sheet: -0.43 (0.29), residues: 297 loop : -1.24 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2830 TYR 0.037 0.001 TYR A2607 PHE 0.028 0.001 PHE A2992 TRP 0.020 0.001 TRP C 453 HIS 0.014 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00343 (21072) covalent geometry : angle 0.62712 (28575) hydrogen bonds : bond 0.03689 ( 1164) hydrogen bonds : angle 4.56011 ( 3432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1608 LEU cc_start: 0.8222 (mt) cc_final: 0.7984 (mp) REVERT: A 1786 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 1879 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 1913 LYS cc_start: 0.9084 (tttt) cc_final: 0.8557 (mtpp) REVERT: A 1987 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: A 2059 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: A 2088 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6484 (mm) REVERT: A 2118 MET cc_start: 0.7933 (tpp) cc_final: 0.6868 (mtt) REVERT: A 2158 LEU cc_start: 0.8066 (tp) cc_final: 0.7716 (tp) REVERT: A 2171 ASP cc_start: 0.7013 (t70) cc_final: 0.5963 (t70) REVERT: A 2232 LYS cc_start: 0.8984 (tptp) cc_final: 0.8722 (tptm) REVERT: A 2270 ASN cc_start: 0.8127 (t0) cc_final: 0.7466 (p0) REVERT: A 2282 ASN cc_start: 0.8418 (m-40) cc_final: 0.8143 (m110) REVERT: A 2300 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: A 2444 ASN cc_start: 0.7713 (t0) cc_final: 0.7479 (t0) REVERT: A 2574 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: A 2680 TYR cc_start: 0.7073 (m-80) cc_final: 0.6469 (m-80) REVERT: A 2830 ARG cc_start: 0.8189 (mpt-90) cc_final: 0.7972 (mmt90) REVERT: A 2844 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: A 2975 ASN cc_start: 0.8750 (m110) cc_final: 0.8485 (m110) REVERT: A 2977 TYR cc_start: 0.7107 (t80) cc_final: 0.6739 (t80) REVERT: A 3413 HIS cc_start: 0.8375 (m90) cc_final: 0.7917 (m-70) REVERT: A 3500 ASP cc_start: 0.8290 (t0) cc_final: 0.7679 (p0) REVERT: A 3616 GLU cc_start: 0.7654 (pp20) cc_final: 0.7443 (pp20) REVERT: A 3717 GLU cc_start: 0.9033 (tp30) cc_final: 0.8420 (pt0) REVERT: A 3875 MET cc_start: 0.8283 (mmt) cc_final: 0.7848 (mmm) REVERT: A 3980 ILE cc_start: 0.8864 (mm) cc_final: 0.8636 (mm) REVERT: C 145 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8277 (mmp-170) REVERT: C 146 ASN cc_start: 0.9085 (p0) cc_final: 0.8589 (p0) REVERT: C 195 GLN cc_start: 0.7101 (tm-30) cc_final: 0.5885 (mt0) REVERT: C 344 LYS cc_start: 0.6432 (tppt) cc_final: 0.5974 (mtpt) REVERT: C 385 TRP cc_start: 0.6395 (m100) cc_final: 0.5451 (m100) REVERT: C 426 ARG cc_start: 0.7615 (ptt180) cc_final: 0.6083 (ttp80) REVERT: C 450 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7855 (mm) REVERT: C 490 ASN cc_start: 0.7014 (m-40) cc_final: 0.6808 (m-40) outliers start: 84 outliers final: 61 residues processed: 320 average time/residue: 0.1408 time to fit residues: 72.2294 Evaluate side-chains 323 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 253 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2138 ASN Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2313 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2653 TRP Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2712 LEU Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2890 THR Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3391 LEU Chi-restraints excluded: chain A residue 3418 ILE Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2138 ASN A2201 HIS A2536 ASN A2598 HIS C 277 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 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 = 0.4144 r_free = 0.4144 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111131 restraints weight = 58461.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111307 restraints weight = 41328.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112755 restraints weight = 27931.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113369 restraints weight = 22660.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113425 restraints weight = 19246.508| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21072 Z= 0.160 Angle : 0.640 12.651 28575 Z= 0.322 Chirality : 0.043 0.187 3303 Planarity : 0.004 0.080 3576 Dihedral : 5.985 119.081 2861 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.04 % Allowed : 22.34 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.17), residues: 2581 helix: 1.30 (0.14), residues: 1372 sheet: -0.49 (0.29), residues: 297 loop : -1.26 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A2606 TYR 0.024 0.001 TYR A2849 PHE 0.027 0.001 PHE A2992 TRP 0.021 0.001 TRP C 453 HIS 0.011 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00367 (21072) covalent geometry : angle 0.64041 (28575) hydrogen bonds : bond 0.03736 ( 1164) hydrogen bonds : angle 4.60269 ( 3432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 259 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1608 LEU cc_start: 0.8229 (mt) cc_final: 0.7994 (mp) REVERT: A 1786 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8791 (mm) REVERT: A 1867 GLN cc_start: 0.7701 (tp40) cc_final: 0.7458 (tp40) REVERT: A 1879 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 1913 LYS cc_start: 0.9103 (tttt) cc_final: 0.8563 (mtpp) REVERT: A 1987 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8442 (m-10) REVERT: A 2059 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: A 2088 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6445 (mm) REVERT: A 2118 MET cc_start: 0.7856 (tpp) cc_final: 0.7394 (tpp) REVERT: A 2158 LEU cc_start: 0.8138 (tp) cc_final: 0.7763 (tp) REVERT: A 2171 ASP cc_start: 0.7056 (t70) cc_final: 0.6036 (t70) REVERT: A 2232 LYS cc_start: 0.8997 (tptp) cc_final: 0.8745 (tptm) REVERT: A 2270 ASN cc_start: 0.8133 (t0) cc_final: 0.7407 (p0) REVERT: A 2282 ASN cc_start: 0.8366 (m-40) cc_final: 0.8143 (m110) REVERT: A 2300 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: A 2444 ASN cc_start: 0.7711 (t0) cc_final: 0.7455 (t0) REVERT: A 2574 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: A 2680 TYR cc_start: 0.6957 (m-80) cc_final: 0.6379 (m-80) REVERT: A 2732 MET cc_start: 0.6659 (tpp) cc_final: 0.6408 (tpp) REVERT: A 2830 ARG cc_start: 0.8190 (mpt-90) cc_final: 0.7896 (mmt90) REVERT: A 2844 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5545 (m-80) REVERT: A 2975 ASN cc_start: 0.8837 (m110) cc_final: 0.8535 (m110) REVERT: A 2977 TYR cc_start: 0.7090 (t80) cc_final: 0.6643 (t80) REVERT: A 3413 HIS cc_start: 0.8334 (m90) cc_final: 0.7848 (m-70) REVERT: A 3454 ASP cc_start: 0.7914 (t0) cc_final: 0.7149 (p0) REVERT: A 3500 ASP cc_start: 0.8308 (t0) cc_final: 0.7731 (p0) REVERT: A 3717 GLU cc_start: 0.9036 (tp30) cc_final: 0.8410 (pt0) REVERT: A 3875 MET cc_start: 0.8360 (mmt) cc_final: 0.7915 (mmm) REVERT: A 3934 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7005 (t60) REVERT: A 3980 ILE cc_start: 0.8841 (mm) cc_final: 0.8612 (mm) REVERT: C 145 ARG cc_start: 0.8885 (ptp-110) cc_final: 0.8271 (mmp-170) REVERT: C 146 ASN cc_start: 0.9086 (p0) cc_final: 0.8626 (p0) REVERT: C 195 GLN cc_start: 0.7053 (tm-30) cc_final: 0.5836 (mt0) REVERT: C 344 LYS cc_start: 0.6459 (tppt) cc_final: 0.6024 (mtpt) REVERT: C 385 TRP cc_start: 0.6407 (m100) cc_final: 0.5516 (m100) REVERT: C 426 ARG cc_start: 0.7638 (ptt180) cc_final: 0.6121 (ttp80) REVERT: C 450 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (mm) REVERT: C 490 ASN cc_start: 0.7145 (m-40) cc_final: 0.6918 (m-40) outliers start: 88 outliers final: 65 residues processed: 320 average time/residue: 0.1418 time to fit residues: 73.2369 Evaluate side-chains 329 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2138 ASN Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2313 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2653 TRP Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2704 PHE Chi-restraints excluded: chain A residue 2712 LEU Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2890 THR Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 2924 THR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3391 LEU Chi-restraints excluded: chain A residue 3418 ILE Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 173 optimal weight: 0.0050 chunk 149 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2138 ASN A3856 HIS ** C 490 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 = 0.4165 r_free = 0.4165 target = 0.144304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111864 restraints weight = 58440.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113274 restraints weight = 37738.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114893 restraints weight = 24322.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.115346 restraints weight = 20081.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.115439 restraints weight = 18094.911| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21072 Z= 0.125 Angle : 0.637 14.926 28575 Z= 0.316 Chirality : 0.042 0.192 3303 Planarity : 0.004 0.102 3576 Dihedral : 5.887 117.171 2861 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.07 % Allowed : 23.53 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.17), residues: 2581 helix: 1.34 (0.14), residues: 1371 sheet: -0.45 (0.29), residues: 301 loop : -1.18 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A2606 TYR 0.021 0.001 TYR A2849 PHE 0.027 0.001 PHE A2992 TRP 0.022 0.001 TRP C 453 HIS 0.006 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00282 (21072) covalent geometry : angle 0.63677 (28575) hydrogen bonds : bond 0.03603 ( 1164) hydrogen bonds : angle 4.49777 ( 3432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1608 LEU cc_start: 0.8266 (mt) cc_final: 0.8041 (mt) REVERT: A 1786 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 1867 GLN cc_start: 0.7702 (tp40) cc_final: 0.7448 (tp40) REVERT: A 1879 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 1913 LYS cc_start: 0.9060 (tttt) cc_final: 0.8523 (mtpp) REVERT: A 1987 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: A 2059 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: A 2088 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6239 (mm) REVERT: A 2118 MET cc_start: 0.7694 (tpp) cc_final: 0.6757 (mtt) REVERT: A 2158 LEU cc_start: 0.8180 (tp) cc_final: 0.7850 (tp) REVERT: A 2171 ASP cc_start: 0.6971 (t70) cc_final: 0.5935 (t70) REVERT: A 2232 LYS cc_start: 0.9002 (tptp) cc_final: 0.8750 (tptm) REVERT: A 2251 ASP cc_start: 0.8804 (p0) cc_final: 0.8589 (p0) REVERT: A 2270 ASN cc_start: 0.8088 (t0) cc_final: 0.7373 (p0) REVERT: A 2300 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: A 2444 ASN cc_start: 0.7614 (t0) cc_final: 0.7368 (t0) REVERT: A 2574 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: A 2680 TYR cc_start: 0.6958 (m-80) cc_final: 0.6405 (m-80) REVERT: A 2732 MET cc_start: 0.6718 (tpp) cc_final: 0.6440 (tpp) REVERT: A 2830 ARG cc_start: 0.8177 (mpt-90) cc_final: 0.7879 (mmt90) REVERT: A 2844 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5674 (m-80) REVERT: A 2975 ASN cc_start: 0.8827 (m110) cc_final: 0.8519 (m110) REVERT: A 2977 TYR cc_start: 0.7043 (t80) cc_final: 0.6624 (t80) REVERT: A 3413 HIS cc_start: 0.8397 (m90) cc_final: 0.7916 (m-70) REVERT: A 3454 ASP cc_start: 0.7946 (t0) cc_final: 0.7202 (p0) REVERT: A 3500 ASP cc_start: 0.8293 (t0) cc_final: 0.7711 (p0) REVERT: A 3875 MET cc_start: 0.8347 (mmt) cc_final: 0.7930 (mmm) REVERT: A 3934 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.6883 (t60) REVERT: A 3980 ILE cc_start: 0.8790 (mm) cc_final: 0.8523 (mm) REVERT: C 145 ARG cc_start: 0.8887 (ptp-110) cc_final: 0.8258 (mmp-170) REVERT: C 146 ASN cc_start: 0.9064 (p0) cc_final: 0.8608 (p0) REVERT: C 195 GLN cc_start: 0.7036 (tm-30) cc_final: 0.5884 (mt0) REVERT: C 274 SER cc_start: 0.7618 (m) cc_final: 0.7341 (p) REVERT: C 344 LYS cc_start: 0.6446 (tppt) cc_final: 0.6085 (ttpt) REVERT: C 385 TRP cc_start: 0.6300 (m100) cc_final: 0.5449 (m100) REVERT: C 426 ARG cc_start: 0.7655 (ptt180) cc_final: 0.6228 (ttp80) REVERT: C 450 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 490 ASN cc_start: 0.7103 (m-40) cc_final: 0.6886 (m-40) outliers start: 67 outliers final: 51 residues processed: 311 average time/residue: 0.1488 time to fit residues: 74.2542 Evaluate side-chains 315 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2138 ASN Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2653 TRP Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2704 PHE Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2844 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2890 THR Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 2924 THR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3391 LEU Chi-restraints excluded: chain A residue 3418 ILE Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 256 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2138 ASN A3472 HIS C 277 GLN C 286 ASN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 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 = 0.4125 r_free = 0.4125 target = 0.141444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109875 restraints weight = 58648.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110437 restraints weight = 35032.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111120 restraints weight = 26889.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.111528 restraints weight = 23687.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.111744 restraints weight = 20479.073| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21072 Z= 0.197 Angle : 0.688 13.353 28575 Z= 0.347 Chirality : 0.044 0.208 3303 Planarity : 0.005 0.105 3576 Dihedral : 6.042 121.838 2861 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.21 % Allowed : 23.85 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.17), residues: 2581 helix: 1.19 (0.14), residues: 1374 sheet: -0.44 (0.29), residues: 310 loop : -1.31 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A2606 TYR 0.021 0.002 TYR A2849 PHE 0.023 0.002 PHE A2302 TRP 0.021 0.002 TRP C 453 HIS 0.010 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00453 (21072) covalent geometry : angle 0.68845 (28575) hydrogen bonds : bond 0.03925 ( 1164) hydrogen bonds : angle 4.66167 ( 3432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 251 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1608 LEU cc_start: 0.8273 (mt) cc_final: 0.8029 (mp) REVERT: A 1786 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8789 (mm) REVERT: A 1839 THR cc_start: 0.8916 (m) cc_final: 0.8707 (m) REVERT: A 1867 GLN cc_start: 0.7885 (tp40) cc_final: 0.7564 (tp40) REVERT: A 1879 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 1913 LYS cc_start: 0.9089 (tttt) cc_final: 0.8565 (mtpp) REVERT: A 1987 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: A 2059 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: A 2088 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6772 (mm) REVERT: A 2118 MET cc_start: 0.7859 (tpp) cc_final: 0.7262 (tpp) REVERT: A 2158 LEU cc_start: 0.8218 (tp) cc_final: 0.7812 (tp) REVERT: A 2171 ASP cc_start: 0.7240 (t70) cc_final: 0.6234 (t70) REVERT: A 2232 LYS cc_start: 0.9025 (tptp) cc_final: 0.8775 (tptm) REVERT: A 2248 LYS cc_start: 0.8193 (pttt) cc_final: 0.7504 (pttp) REVERT: A 2251 ASP cc_start: 0.8930 (p0) cc_final: 0.8719 (p0) REVERT: A 2270 ASN cc_start: 0.8193 (t0) cc_final: 0.7387 (p0) REVERT: A 2300 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: A 2444 ASN cc_start: 0.7792 (t0) cc_final: 0.7541 (t0) REVERT: A 2574 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: A 2732 MET cc_start: 0.6844 (tpp) cc_final: 0.6142 (tpp) REVERT: A 2830 ARG cc_start: 0.8229 (mpt-90) cc_final: 0.7915 (mmt90) REVERT: A 2977 TYR cc_start: 0.7274 (t80) cc_final: 0.6757 (t80) REVERT: A 3413 HIS cc_start: 0.8462 (m90) cc_final: 0.7926 (m-70) REVERT: A 3472 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6746 (t-90) REVERT: A 3500 ASP cc_start: 0.8391 (t0) cc_final: 0.7768 (p0) REVERT: A 3856 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5434 (t-90) REVERT: A 3875 MET cc_start: 0.8387 (mmt) cc_final: 0.7902 (mmm) REVERT: A 3980 ILE cc_start: 0.8844 (mm) cc_final: 0.8618 (mm) REVERT: C 145 ARG cc_start: 0.8881 (ptp-110) cc_final: 0.8265 (mmp-170) REVERT: C 146 ASN cc_start: 0.9195 (p0) cc_final: 0.8732 (p0) REVERT: C 344 LYS cc_start: 0.6478 (tppt) cc_final: 0.6077 (mtpt) REVERT: C 385 TRP cc_start: 0.6320 (m100) cc_final: 0.5515 (m100) REVERT: C 426 ARG cc_start: 0.7772 (ptt180) cc_final: 0.6211 (ttp80) REVERT: C 490 ASN cc_start: 0.7251 (m-40) cc_final: 0.7023 (m-40) outliers start: 70 outliers final: 53 residues processed: 300 average time/residue: 0.1422 time to fit residues: 68.8501 Evaluate side-chains 306 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1528 GLU Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1879 ILE Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2451 THR Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2556 ILE Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2621 GLU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2653 TRP Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2704 PHE Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2913 ILE Chi-restraints excluded: chain A residue 2924 THR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3391 LEU Chi-restraints excluded: chain A residue 3418 ILE Chi-restraints excluded: chain A residue 3462 ILE Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3632 LEU Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3916 PHE Chi-restraints excluded: chain A residue 3934 TRP Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 179 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 226 optimal weight: 0.3980 chunk 178 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2138 ASN C 286 ASN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 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 = 0.4130 r_free = 0.4130 target = 0.141767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110444 restraints weight = 58466.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110481 restraints weight = 38278.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111431 restraints weight = 27604.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112110 restraints weight = 23605.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112321 restraints weight = 19925.470| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 21072 Z= 0.243 Angle : 0.892 59.200 28575 Z= 0.508 Chirality : 0.046 0.817 3303 Planarity : 0.006 0.217 3576 Dihedral : 6.058 121.802 2861 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.35 % Allowed : 23.76 % Favored : 72.89 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.17), residues: 2581 helix: 1.19 (0.14), residues: 1374 sheet: -0.44 (0.29), residues: 310 loop : -1.33 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2606 TYR 0.020 0.001 TYR A2607 PHE 0.022 0.002 PHE A2302 TRP 0.019 0.001 TRP C 453 HIS 0.369 0.005 HIS A3472 Details of bonding type rmsd covalent geometry : bond 0.00494 (21072) covalent geometry : angle 0.89246 (28575) hydrogen bonds : bond 0.03901 ( 1164) hydrogen bonds : angle 4.65718 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.48 seconds wall clock time: 62 minutes 1.22 seconds (3721.22 seconds total)