Starting phenix.real_space_refine on Fri Jun 20 08:17:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn4_44721/06_2025/9bn4_44721.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 115 5.16 5 C 14683 2.51 5 N 3983 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23078 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2855, 22962 Classifications: {'peptide': 2855} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 129, 'TRANS': 2725} Chain breaks: 6 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 14.61, per 1000 atoms: 0.63 Number of scatterers: 23078 At special positions: 0 Unit cell: (127.184, 169.578, 151.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 10 15.00 O 4287 8.00 N 3983 7.00 C 14683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 3.3 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 20 sheets defined 62.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 1463 through 1470 removed outlier: 3.682A pdb=" N TRP A1470 " --> pdb=" O ILE A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.992A pdb=" N LYS A1496 " --> pdb=" O ASP A1492 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A1497 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1554 removed outlier: 3.840A pdb=" N LEU A1521 " --> pdb=" O GLU A1517 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.616A pdb=" N VAL A1591 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A1592 " --> pdb=" O VAL A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1658 removed outlier: 4.173A pdb=" N LEU A1650 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A1652 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A1655 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS A1656 " --> pdb=" O LYS A1652 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.967A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1776 through 1798 removed outlier: 3.787A pdb=" N SER A1780 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1825 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 removed outlier: 3.555A pdb=" N GLN A1855 " --> pdb=" O ASP A1852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1852 through 1855' Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 4.007A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.562A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 removed outlier: 3.796A pdb=" N LYS A2033 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2077 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.610A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.001A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.902A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2289 Processing helix chain 'A' and resid 2308 through 2320 removed outlier: 5.435A pdb=" N ASN A2314 " --> pdb=" O GLU A2310 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.522A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2442 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.639A pdb=" N LEU A2458 " --> pdb=" O CYS A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2502 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.608A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.836A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.596A pdb=" N THR A2604 " --> pdb=" O GLY A2600 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.170A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.914A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.650A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2783 removed outlier: 3.619A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 4.225A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2886 through 2904 Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3013 removed outlier: 3.675A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 removed outlier: 4.208A pdb=" N PHE A3021 " --> pdb=" O PRO A3018 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.592A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3516 removed outlier: 3.745A pdb=" N ALA A3477 " --> pdb=" O ASN A3473 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.779A pdb=" N TYR A3552 " --> pdb=" O ALA A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.635A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A3641 " --> pdb=" O VAL A3638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3637 through 3641' Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.700A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3736 removed outlier: 3.753A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A3736 " --> pdb=" O LEU A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 removed outlier: 3.561A pdb=" N LEU A3740 " --> pdb=" O GLY A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3763 through 3786 removed outlier: 3.997A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3801 Processing helix chain 'A' and resid 3801 through 3817 removed outlier: 3.696A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3820 No H-bonds generated for 'chain 'A' and resid 3818 through 3820' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.609A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.522A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3873 removed outlier: 4.048A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3911 through 3914 Processing helix chain 'A' and resid 3928 through 3941 removed outlier: 3.730A pdb=" N LEU A3941 " --> pdb=" O ARG A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.539A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 4.167A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.906A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.863A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.730A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.819A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4251 through 4256 removed outlier: 4.342A pdb=" N ARG A4255 " --> pdb=" O ILE A4251 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A4256 " --> pdb=" O TYR A4252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4251 through 4256' Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.866A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4345 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4405 removed outlier: 3.514A pdb=" N ILE A4405 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.899A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4500 through 4507 Processing helix chain 'A' and resid 4516 through 4531 Processing helix chain 'A' and resid 4532 through 4534 No H-bonds generated for 'chain 'A' and resid 4532 through 4534' Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.516A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A4639 " --> pdb=" O PHE A4635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1479 Processing sheet with id=AA2, first strand: chain 'A' and resid 1664 through 1666 removed outlier: 3.516A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.417A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 3.525A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.468A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2248 through 2254 removed outlier: 3.594A pdb=" N TRP A2300 " --> pdb=" O VAL A2250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 6.213A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP A2664 " --> pdb=" O VAL A2618 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU A2620 " --> pdb=" O ASP A2664 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A2709 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 4.270A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2872 through 2873 removed outlier: 4.298A pdb=" N LEU A2872 " --> pdb=" O VAL A2884 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.518A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.440A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 removed outlier: 3.534A pdb=" N ARG A3654 " --> pdb=" O LEU A3661 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A3661 " --> pdb=" O ARG A3654 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A3656 " --> pdb=" O ARG A3659 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 Processing sheet with id=AB9, first strand: chain 'A' and resid 4285 through 4288 removed outlier: 3.830A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A4287 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A4292 " --> pdb=" O LYS A4287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4539 through 4545 removed outlier: 3.764A pdb=" N VAL A4560 " --> pdb=" O THR A4588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.901A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1316 hydrogen bonds defined for protein. 3852 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: 15.01 Time building geometry restraints manager: 7.95 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: 7570 1.34 - 1.46: 4824 1.46 - 1.58: 10978 1.58 - 1.70: 14 1.70 - 1.82: 192 Bond restraints: 23578 Sorted by residual: bond pdb=" CG PRO A2328 " pdb=" CD PRO A2328 " ideal model delta sigma weight residual 1.503 1.298 0.205 3.40e-02 8.65e+02 3.62e+01 bond pdb=" N ASP A3045 " pdb=" CA ASP A3045 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.01e+00 bond pdb=" CG PRO A3137 " pdb=" CD PRO A3137 " ideal model delta sigma weight residual 1.503 1.411 0.092 3.40e-02 8.65e+02 7.25e+00 bond pdb=" N SER A3046 " pdb=" CA SER A3046 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 6.94e+00 bond pdb=" N LEU A3044 " pdb=" CA LEU A3044 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.28e+00 ... (remaining 23573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 31813 3.48 - 6.96: 147 6.96 - 10.44: 17 10.44 - 13.92: 4 13.92 - 17.41: 4 Bond angle restraints: 31985 Sorted by residual: angle pdb=" N PRO A2328 " pdb=" CD PRO A2328 " pdb=" CG PRO A2328 " ideal model delta sigma weight residual 103.20 85.79 17.41 1.50e+00 4.44e-01 1.35e+02 angle pdb=" CA PRO A2328 " pdb=" N PRO A2328 " pdb=" CD PRO A2328 " ideal model delta sigma weight residual 112.00 97.70 14.30 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N PRO A2714 " pdb=" CD PRO A2714 " pdb=" CG PRO A2714 " ideal model delta sigma weight residual 103.20 90.54 12.66 1.50e+00 4.44e-01 7.12e+01 angle pdb=" CA PRO A2714 " pdb=" CB PRO A2714 " pdb=" CG PRO A2714 " ideal model delta sigma weight residual 104.50 89.40 15.10 1.90e+00 2.77e-01 6.32e+01 angle pdb=" CA PRO A2714 " pdb=" N PRO A2714 " pdb=" CD PRO A2714 " ideal model delta sigma weight residual 112.00 101.93 10.07 1.40e+00 5.10e-01 5.17e+01 ... (remaining 31980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.65: 12864 18.65 - 37.30: 1151 37.30 - 55.96: 218 55.96 - 74.61: 52 74.61 - 93.26: 21 Dihedral angle restraints: 14306 sinusoidal: 5944 harmonic: 8362 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 33.26 -93.26 1 2.00e+01 2.50e-03 2.54e+01 dihedral pdb=" CA ALA A2866 " pdb=" C ALA A2866 " pdb=" N MET A2867 " pdb=" CA MET A2867 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU A4106 " pdb=" C LEU A4106 " pdb=" N MET A4107 " pdb=" CA MET A4107 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 14303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2580 0.041 - 0.082: 761 0.082 - 0.123: 226 0.123 - 0.164: 28 0.164 - 0.205: 5 Chirality restraints: 3600 Sorted by residual: chirality pdb=" CB THR A4588 " pdb=" CA THR A4588 " pdb=" OG1 THR A4588 " pdb=" CG2 THR A4588 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A3039 " pdb=" N LYS A3039 " pdb=" C LYS A3039 " pdb=" CB LYS A3039 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB ILE A1698 " pdb=" CA ILE A1698 " pdb=" CG1 ILE A1698 " pdb=" CG2 ILE A1698 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 3597 not shown) Planarity restraints: 4087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3642 " -0.067 5.00e-02 4.00e+02 1.00e-01 1.62e+01 pdb=" N PRO A3643 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A3643 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A3643 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2327 " 0.062 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A2328 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A2328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2328 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A3038 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLN A3038 " 0.051 2.00e-02 2.50e+03 pdb=" O GLN A3038 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A3039 " -0.017 2.00e-02 2.50e+03 ... (remaining 4084 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 302 2.66 - 3.22: 22678 3.22 - 3.78: 37341 3.78 - 4.34: 50582 4.34 - 4.90: 81967 Nonbonded interactions: 192870 Sorted by model distance: nonbonded pdb=" OD1 ASN A2987 " pdb=" ND2 ASN A3061 " model vdw 2.098 3.120 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.107 3.040 nonbonded pdb=" OG SER A2099 " pdb=" OG SER A2140 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A2370 " pdb=" OD1 ASP A2372 " model vdw 2.191 3.040 nonbonded pdb=" O ILE A3948 " pdb=" NE2 GLN A3952 " model vdw 2.194 3.120 ... (remaining 192865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.080 Extract box with map and model: 1.220 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 64.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.004 0.205 23578 Z= 0.170 Angle : 0.713 17.406 31985 Z= 0.379 Chirality : 0.042 0.205 3600 Planarity : 0.005 0.100 4087 Dihedral : 14.831 93.262 8872 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.32 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2841 helix: 1.62 (0.13), residues: 1560 sheet: -0.99 (0.31), residues: 259 loop : -0.70 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A2500 HIS 0.011 0.001 HIS A2637 PHE 0.038 0.002 PHE A2606 TYR 0.030 0.002 TYR A2748 ARG 0.010 0.001 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.13983 ( 1316) hydrogen bonds : angle 5.75695 ( 3852) covalent geometry : bond 0.00387 (23578) covalent geometry : angle 0.71300 (31985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 LEU cc_start: 0.7876 (tt) cc_final: 0.7374 (mm) REVERT: A 1738 TYR cc_start: 0.7760 (t80) cc_final: 0.7503 (t80) REVERT: A 2074 LYS cc_start: 0.8318 (tppt) cc_final: 0.7866 (ttmt) REVERT: A 2187 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7590 (tm130) REVERT: A 2671 MET cc_start: 0.7943 (mtt) cc_final: 0.7676 (mtm) REVERT: A 2779 MET cc_start: 0.8615 (mtp) cc_final: 0.8403 (mtm) REVERT: A 3952 GLN cc_start: 0.4235 (mp-120) cc_final: 0.4007 (pm20) REVERT: A 4066 ILE cc_start: 0.7628 (mm) cc_final: 0.7354 (pp) REVERT: A 4127 THR cc_start: 0.7705 (m) cc_final: 0.7397 (p) REVERT: A 4259 GLU cc_start: 0.7764 (pt0) cc_final: 0.7456 (tt0) REVERT: A 4283 LYS cc_start: 0.7932 (mttp) cc_final: 0.7444 (mtpp) REVERT: A 4460 LEU cc_start: 0.7410 (tp) cc_final: 0.7192 (tt) REVERT: A 4502 LYS cc_start: 0.6672 (mmtm) cc_final: 0.5838 (mppt) REVERT: A 4630 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6270 (mm-30) outliers start: 1 outliers final: 1 residues processed: 388 average time/residue: 1.2968 time to fit residues: 584.3622 Evaluate side-chains 278 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1611 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 115 optimal weight: 0.0770 chunk 223 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1755 GLN A1894 GLN A1922 GLN A2346 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2473 ASN A2485 GLN A2637 HIS ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3709 GLN A3830 GLN A3952 GLN A4114 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.174737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144961 restraints weight = 32660.559| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.13 r_work: 0.3721 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23578 Z= 0.135 Angle : 0.616 9.198 31985 Z= 0.309 Chirality : 0.042 0.192 3600 Planarity : 0.005 0.074 4087 Dihedral : 6.887 93.598 3195 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 1.93 % Allowed : 8.70 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2841 helix: 1.72 (0.13), residues: 1607 sheet: -0.99 (0.32), residues: 244 loop : -0.78 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2845 HIS 0.007 0.001 HIS A2637 PHE 0.032 0.002 PHE A4482 TYR 0.025 0.002 TYR A2748 ARG 0.008 0.001 ARG A2896 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1316) hydrogen bonds : angle 4.50409 ( 3852) covalent geometry : bond 0.00299 (23578) covalent geometry : angle 0.61641 (31985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TRP cc_start: 0.6895 (OUTLIER) cc_final: 0.6601 (t-100) REVERT: A 1679 ARG cc_start: 0.7747 (ptp90) cc_final: 0.7534 (ptm-80) REVERT: A 1738 TYR cc_start: 0.7742 (t80) cc_final: 0.7308 (t80) REVERT: A 1983 ARG cc_start: 0.7048 (ttm-80) cc_final: 0.6518 (ttt180) REVERT: A 2074 LYS cc_start: 0.8332 (tppt) cc_final: 0.7694 (ttmt) REVERT: A 2187 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7830 (tm130) REVERT: A 2665 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 2671 MET cc_start: 0.7845 (mtt) cc_final: 0.7565 (mtm) REVERT: A 2676 THR cc_start: 0.8319 (p) cc_final: 0.7569 (t) REVERT: A 2779 MET cc_start: 0.8728 (mtp) cc_final: 0.8481 (mtp) REVERT: A 3030 MET cc_start: 0.7048 (mmm) cc_final: 0.6621 (mmm) REVERT: A 3497 LYS cc_start: 0.6596 (mmpt) cc_final: 0.5912 (mmpt) REVERT: A 3642 ASP cc_start: 0.8665 (t0) cc_final: 0.8457 (t0) REVERT: A 3786 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 3801 TYR cc_start: 0.7243 (m-10) cc_final: 0.7019 (m-10) REVERT: A 4127 THR cc_start: 0.7856 (m) cc_final: 0.7503 (p) REVERT: A 4129 GLU cc_start: 0.7756 (tp30) cc_final: 0.7053 (tm-30) REVERT: A 4259 GLU cc_start: 0.7560 (pt0) cc_final: 0.7195 (tt0) REVERT: A 4276 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7044 (ppt170) REVERT: A 4502 LYS cc_start: 0.6383 (mmtm) cc_final: 0.5616 (mppt) REVERT: A 4630 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6349 (mm-30) outliers start: 49 outliers final: 24 residues processed: 372 average time/residue: 1.2632 time to fit residues: 546.6696 Evaluate side-chains 315 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1470 TRP Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4232 ASN Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 279 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS A4114 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4232 ASN A4386 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.173728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.144119 restraints weight = 32635.642| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.12 r_work: 0.3706 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23578 Z= 0.122 Angle : 0.567 10.379 31985 Z= 0.282 Chirality : 0.040 0.172 3600 Planarity : 0.004 0.063 4087 Dihedral : 6.412 88.654 3195 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 2.36 % Allowed : 11.73 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2841 helix: 1.89 (0.13), residues: 1608 sheet: -0.89 (0.33), residues: 242 loop : -0.75 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2845 HIS 0.006 0.001 HIS A2588 PHE 0.030 0.001 PHE A4482 TYR 0.021 0.001 TYR A2748 ARG 0.008 0.000 ARG A2896 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1316) hydrogen bonds : angle 4.25131 ( 3852) covalent geometry : bond 0.00269 (23578) covalent geometry : angle 0.56669 (31985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TRP cc_start: 0.6882 (OUTLIER) cc_final: 0.6496 (t-100) REVERT: A 1537 TRP cc_start: 0.8342 (t-100) cc_final: 0.7976 (t60) REVERT: A 1876 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7729 (mm110) REVERT: A 1983 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6751 (ttt-90) REVERT: A 2074 LYS cc_start: 0.8267 (tppt) cc_final: 0.7625 (ttmt) REVERT: A 2187 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7757 (tm130) REVERT: A 2491 GLN cc_start: 0.8241 (mt0) cc_final: 0.7880 (mt0) REVERT: A 2510 MET cc_start: 0.8084 (mmt) cc_final: 0.7698 (mmt) REVERT: A 2606 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 2665 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6638 (mm-30) REVERT: A 2702 LYS cc_start: 0.8240 (tttp) cc_final: 0.8028 (tttt) REVERT: A 2779 MET cc_start: 0.8762 (mtp) cc_final: 0.8550 (mtp) REVERT: A 3030 MET cc_start: 0.7211 (mmm) cc_final: 0.6794 (mmm) REVERT: A 3113 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: A 3487 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5703 (pm20) REVERT: A 3497 LYS cc_start: 0.6669 (mmpt) cc_final: 0.6344 (tptp) REVERT: A 3601 MET cc_start: 0.8615 (mmm) cc_final: 0.8123 (mmm) REVERT: A 3637 ASP cc_start: 0.8083 (m-30) cc_final: 0.7768 (m-30) REVERT: A 3786 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7383 (pt0) REVERT: A 3873 ARG cc_start: 0.7412 (tpp-160) cc_final: 0.7199 (tpp-160) REVERT: A 4092 ARG cc_start: 0.6233 (mmp80) cc_final: 0.5817 (ptp90) REVERT: A 4113 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 4127 THR cc_start: 0.7890 (m) cc_final: 0.7547 (p) REVERT: A 4129 GLU cc_start: 0.7552 (tp30) cc_final: 0.7031 (tm-30) REVERT: A 4259 GLU cc_start: 0.7624 (pt0) cc_final: 0.7311 (tt0) REVERT: A 4415 ARG cc_start: 0.6570 (ttm170) cc_final: 0.6216 (ptm160) REVERT: A 4502 LYS cc_start: 0.6309 (mmtm) cc_final: 0.5504 (mppt) REVERT: A 4506 ASN cc_start: 0.7996 (m110) cc_final: 0.7789 (m110) outliers start: 60 outliers final: 31 residues processed: 342 average time/residue: 1.2551 time to fit residues: 501.2316 Evaluate side-chains 318 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 281 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1470 TRP Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1876 GLN Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2585 LEU Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4232 ASN Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 224 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 228 optimal weight: 0.0970 chunk 232 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 231 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A1894 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2463 HIS A2677 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3744 GLN A3852 HIS A4114 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4386 ASN A4508 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135643 restraints weight = 33389.244| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.37 r_work: 0.3539 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23578 Z= 0.157 Angle : 0.591 10.071 31985 Z= 0.295 Chirality : 0.041 0.175 3600 Planarity : 0.004 0.061 4087 Dihedral : 6.409 84.962 3193 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 13.23 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2841 helix: 1.81 (0.13), residues: 1615 sheet: -0.80 (0.33), residues: 252 loop : -0.67 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2845 HIS 0.005 0.001 HIS A2857 PHE 0.033 0.002 PHE A4482 TYR 0.028 0.002 TYR A2748 ARG 0.004 0.000 ARG A2797 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 1316) hydrogen bonds : angle 4.19114 ( 3852) covalent geometry : bond 0.00370 (23578) covalent geometry : angle 0.59116 (31985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 312 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1470 TRP cc_start: 0.6964 (OUTLIER) cc_final: 0.6524 (t-100) REVERT: A 1537 TRP cc_start: 0.8209 (t-100) cc_final: 0.7987 (t60) REVERT: A 1983 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6600 (ttt-90) REVERT: A 2074 LYS cc_start: 0.8037 (tppt) cc_final: 0.7300 (ttmt) REVERT: A 2510 MET cc_start: 0.8344 (mmt) cc_final: 0.8136 (mmt) REVERT: A 2665 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 2671 MET cc_start: 0.8162 (mtp) cc_final: 0.7854 (mmm) REVERT: A 2779 MET cc_start: 0.8649 (mtp) cc_final: 0.8396 (mtp) REVERT: A 2882 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7743 (pp) REVERT: A 2998 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (m-40) REVERT: A 3030 MET cc_start: 0.7259 (mmm) cc_final: 0.6789 (mmm) REVERT: A 3114 ASP cc_start: 0.7911 (t70) cc_final: 0.7217 (m-30) REVERT: A 3487 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5696 (pm20) REVERT: A 3497 LYS cc_start: 0.6603 (mmpt) cc_final: 0.6392 (ttpt) REVERT: A 3553 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 3637 ASP cc_start: 0.7942 (m-30) cc_final: 0.7608 (m-30) REVERT: A 3741 ARG cc_start: 0.4937 (OUTLIER) cc_final: 0.4341 (ptp90) REVERT: A 3786 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7271 (pt0) REVERT: A 3873 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6837 (tpp-160) REVERT: A 3967 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6923 (pt0) REVERT: A 4054 HIS cc_start: 0.6814 (m90) cc_final: 0.6558 (m90) REVERT: A 4113 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 4127 THR cc_start: 0.7911 (m) cc_final: 0.7505 (p) REVERT: A 4129 GLU cc_start: 0.7386 (tp30) cc_final: 0.7115 (tp30) REVERT: A 4259 GLU cc_start: 0.7410 (pt0) cc_final: 0.7031 (tt0) REVERT: A 4415 ARG cc_start: 0.6554 (ttm170) cc_final: 0.6067 (ptm160) REVERT: A 4502 LYS cc_start: 0.6256 (mmtm) cc_final: 0.5469 (mppt) outliers start: 81 outliers final: 35 residues processed: 356 average time/residue: 1.2594 time to fit residues: 524.2664 Evaluate side-chains 319 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1470 TRP Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3553 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3873 ARG Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 112 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 131 optimal weight: 0.0570 chunk 161 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A1894 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138362 restraints weight = 33009.670| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.33 r_work: 0.3541 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23578 Z= 0.132 Angle : 0.569 10.679 31985 Z= 0.282 Chirality : 0.040 0.179 3600 Planarity : 0.004 0.059 4087 Dihedral : 6.266 89.477 3193 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 3.19 % Allowed : 15.00 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2841 helix: 1.87 (0.13), residues: 1613 sheet: -0.78 (0.33), residues: 244 loop : -0.58 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2845 HIS 0.005 0.001 HIS A2857 PHE 0.035 0.002 PHE A4482 TYR 0.024 0.001 TYR A2748 ARG 0.006 0.000 ARG A4301 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1316) hydrogen bonds : angle 4.07755 ( 3852) covalent geometry : bond 0.00301 (23578) covalent geometry : angle 0.56864 (31985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1470 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.6597 (m100) REVERT: A 1597 VAL cc_start: 0.6586 (t) cc_final: 0.6366 (m) REVERT: A 1599 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7370 (tpp-160) REVERT: A 1819 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.8209 (tmm160) REVERT: A 1983 ARG cc_start: 0.7046 (ttm-80) cc_final: 0.6803 (ttt-90) REVERT: A 2074 LYS cc_start: 0.8173 (tppt) cc_final: 0.7450 (ttmt) REVERT: A 2315 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 2373 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8003 (ptp) REVERT: A 2665 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6557 (mm-30) REVERT: A 2702 LYS cc_start: 0.8448 (tttp) cc_final: 0.8210 (tttt) REVERT: A 2779 MET cc_start: 0.8738 (mtp) cc_final: 0.8480 (mtp) REVERT: A 2798 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: A 2998 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: A 3030 MET cc_start: 0.7227 (mmm) cc_final: 0.6859 (mmm) REVERT: A 3487 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5685 (pm20) REVERT: A 3497 LYS cc_start: 0.6468 (mmpt) cc_final: 0.6248 (ttpt) REVERT: A 3551 GLU cc_start: 0.8081 (mp0) cc_final: 0.7768 (tt0) REVERT: A 3553 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (mt) REVERT: A 3637 ASP cc_start: 0.7955 (m-30) cc_final: 0.7662 (m-30) REVERT: A 3732 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 3786 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7408 (pt0) REVERT: A 3873 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6953 (tpp-160) REVERT: A 3967 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: A 4092 ARG cc_start: 0.6033 (ptp-110) cc_final: 0.5730 (ptm160) REVERT: A 4113 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 4127 THR cc_start: 0.8037 (m) cc_final: 0.7628 (p) REVERT: A 4129 GLU cc_start: 0.7565 (tp30) cc_final: 0.7311 (tp30) REVERT: A 4259 GLU cc_start: 0.7617 (pt0) cc_final: 0.7241 (tt0) REVERT: A 4283 LYS cc_start: 0.8085 (mttp) cc_final: 0.7520 (mtpt) REVERT: A 4415 ARG cc_start: 0.6678 (ttm170) cc_final: 0.6226 (ptm160) REVERT: A 4502 LYS cc_start: 0.6388 (mmtm) cc_final: 0.5668 (mppt) outliers start: 81 outliers final: 32 residues processed: 351 average time/residue: 1.4772 time to fit residues: 609.0623 Evaluate side-chains 321 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1470 TRP Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2373 MET Chi-restraints excluded: chain A residue 2672 ASP Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2798 GLU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3553 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3873 ARG Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 259 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 238 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 205 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A1894 GLN A2079 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN A3155 HIS ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136595 restraints weight = 32704.432| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.30 r_work: 0.3520 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23578 Z= 0.143 Angle : 0.578 10.629 31985 Z= 0.286 Chirality : 0.041 0.193 3600 Planarity : 0.004 0.055 4087 Dihedral : 6.173 83.773 3193 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 16.06 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2841 helix: 1.82 (0.13), residues: 1620 sheet: -0.72 (0.34), residues: 239 loop : -0.58 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2845 HIS 0.004 0.001 HIS A2445 PHE 0.037 0.002 PHE A4482 TYR 0.023 0.001 TYR A2748 ARG 0.004 0.000 ARG A3486 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 1316) hydrogen bonds : angle 4.08268 ( 3852) covalent geometry : bond 0.00336 (23578) covalent geometry : angle 0.57834 (31985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1597 VAL cc_start: 0.6504 (t) cc_final: 0.6282 (m) REVERT: A 1599 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7233 (tpp-160) REVERT: A 1819 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8219 (tmm160) REVERT: A 1983 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6573 (ttt180) REVERT: A 2074 LYS cc_start: 0.8213 (tppt) cc_final: 0.7502 (ttmt) REVERT: A 2315 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 2665 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6308 (mm-30) REVERT: A 2779 MET cc_start: 0.8745 (mtp) cc_final: 0.8486 (mtp) REVERT: A 2798 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: A 2858 PHE cc_start: 0.5153 (t80) cc_final: 0.4515 (t80) REVERT: A 2860 ASN cc_start: 0.8270 (m-40) cc_final: 0.8061 (m-40) REVERT: A 2998 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: A 3487 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5642 (pm20) REVERT: A 3497 LYS cc_start: 0.6591 (mmpt) cc_final: 0.6339 (ttpt) REVERT: A 3551 GLU cc_start: 0.8051 (mp0) cc_final: 0.7703 (tt0) REVERT: A 3637 ASP cc_start: 0.7874 (m-30) cc_final: 0.7603 (m-30) REVERT: A 3741 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4429 (ptp-170) REVERT: A 3786 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7422 (pt0) REVERT: A 3967 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7095 (pt0) REVERT: A 4054 HIS cc_start: 0.6756 (m90) cc_final: 0.6429 (m90) REVERT: A 4092 ARG cc_start: 0.6138 (ptp-110) cc_final: 0.5923 (ptm160) REVERT: A 4113 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 4129 GLU cc_start: 0.7556 (tp30) cc_final: 0.7313 (tp30) REVERT: A 4259 GLU cc_start: 0.7574 (pt0) cc_final: 0.7228 (tt0) REVERT: A 4415 ARG cc_start: 0.6776 (ttm170) cc_final: 0.6232 (ptm160) REVERT: A 4502 LYS cc_start: 0.6294 (mmtm) cc_final: 0.5577 (mppt) outliers start: 75 outliers final: 39 residues processed: 352 average time/residue: 1.3086 time to fit residues: 535.7568 Evaluate side-chains 322 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1599 ARG Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2672 ASP Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2798 GLU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 36 optimal weight: 0.0570 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A1894 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2485 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2918 HIS ** A3061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN A3155 HIS ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132622 restraints weight = 33093.434| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.33 r_work: 0.3505 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23578 Z= 0.149 Angle : 0.599 11.781 31985 Z= 0.296 Chirality : 0.041 0.260 3600 Planarity : 0.004 0.055 4087 Dihedral : 6.142 75.270 3193 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 2.95 % Allowed : 17.17 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2841 helix: 1.84 (0.13), residues: 1609 sheet: -0.64 (0.34), residues: 229 loop : -0.53 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A2845 HIS 0.005 0.001 HIS A2445 PHE 0.037 0.002 PHE A4482 TYR 0.021 0.002 TYR A2748 ARG 0.004 0.000 ARG A2797 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1316) hydrogen bonds : angle 4.09447 ( 3852) covalent geometry : bond 0.00348 (23578) covalent geometry : angle 0.59886 (31985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 304 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: A 1599 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (tpp-160) REVERT: A 1819 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8168 (tmm160) REVERT: A 1933 ASP cc_start: 0.5937 (m-30) cc_final: 0.5369 (p0) REVERT: A 1936 PHE cc_start: 0.7379 (t80) cc_final: 0.7169 (t80) REVERT: A 1983 ARG cc_start: 0.6930 (ttm-80) cc_final: 0.6458 (ttt180) REVERT: A 2074 LYS cc_start: 0.8373 (tppt) cc_final: 0.7706 (ttmt) REVERT: A 2315 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7715 (mm) REVERT: A 2349 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8465 (ptmm) REVERT: A 2665 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6416 (mm-30) REVERT: A 2779 MET cc_start: 0.8740 (mtp) cc_final: 0.8478 (mtp) REVERT: A 2858 PHE cc_start: 0.5257 (t80) cc_final: 0.4539 (t80) REVERT: A 2998 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8005 (m-40) REVERT: A 3487 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5568 (pm20) REVERT: A 3497 LYS cc_start: 0.6738 (mmpt) cc_final: 0.6533 (ttpt) REVERT: A 3551 GLU cc_start: 0.8075 (mp0) cc_final: 0.7678 (tt0) REVERT: A 3601 MET cc_start: 0.8590 (mmm) cc_final: 0.8387 (mmp) REVERT: A 3637 ASP cc_start: 0.7870 (m-30) cc_final: 0.7638 (m-30) REVERT: A 3741 ARG cc_start: 0.5149 (OUTLIER) cc_final: 0.4466 (ptp90) REVERT: A 3786 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7417 (pt0) REVERT: A 3967 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: A 4054 HIS cc_start: 0.6795 (m90) cc_final: 0.6514 (m90) REVERT: A 4071 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6773 (pt) REVERT: A 4092 ARG cc_start: 0.6069 (ptp-110) cc_final: 0.5864 (ptm160) REVERT: A 4129 GLU cc_start: 0.7529 (tp30) cc_final: 0.7281 (tp30) REVERT: A 4259 GLU cc_start: 0.7583 (pt0) cc_final: 0.7244 (tt0) REVERT: A 4283 LYS cc_start: 0.8035 (mttp) cc_final: 0.7514 (mtpt) REVERT: A 4301 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7790 (pmm-80) REVERT: A 4415 ARG cc_start: 0.6731 (ttm170) cc_final: 0.6136 (ptm160) REVERT: A 4460 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.5889 (tt) REVERT: A 4502 LYS cc_start: 0.6471 (mmtm) cc_final: 0.5746 (mppt) outliers start: 75 outliers final: 38 residues processed: 348 average time/residue: 1.3447 time to fit residues: 548.7989 Evaluate side-chains 324 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1599 ARG Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2672 ASP Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 48 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 258 optimal weight: 0.3980 chunk 272 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 256 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2875 ASN ** A3061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN A3595 GLN ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.164625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133529 restraints weight = 32764.398| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.31 r_work: 0.3538 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23578 Z= 0.129 Angle : 0.592 13.405 31985 Z= 0.290 Chirality : 0.041 0.213 3600 Planarity : 0.004 0.054 4087 Dihedral : 6.048 72.272 3193 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 2.83 % Allowed : 17.87 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2841 helix: 1.86 (0.13), residues: 1609 sheet: -0.62 (0.34), residues: 229 loop : -0.52 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A3974 HIS 0.004 0.001 HIS A2445 PHE 0.037 0.001 PHE A4482 TYR 0.027 0.001 TYR A2748 ARG 0.006 0.000 ARG A2977 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1316) hydrogen bonds : angle 4.04678 ( 3852) covalent geometry : bond 0.00294 (23578) covalent geometry : angle 0.59201 (31985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 3.084 Fit side-chains revert: symmetry clash REVERT: A 1599 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7335 (tpp-160) REVERT: A 1738 TYR cc_start: 0.7729 (t80) cc_final: 0.7526 (t80) REVERT: A 1792 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7263 (mt) REVERT: A 1819 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.8135 (tmm160) REVERT: A 1933 ASP cc_start: 0.6426 (m-30) cc_final: 0.5640 (p0) REVERT: A 1998 THR cc_start: 0.8121 (p) cc_final: 0.7883 (t) REVERT: A 2074 LYS cc_start: 0.8372 (tppt) cc_final: 0.7701 (ttmt) REVERT: A 2315 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 2349 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8448 (ptmm) REVERT: A 2665 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6181 (mm-30) REVERT: A 2767 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7455 (mp0) REVERT: A 2779 MET cc_start: 0.8750 (mtp) cc_final: 0.8509 (mtp) REVERT: A 2858 PHE cc_start: 0.5196 (t80) cc_final: 0.4451 (t80) REVERT: A 2867 MET cc_start: 0.5400 (pmm) cc_final: 0.5121 (ppp) REVERT: A 2998 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8028 (m-40) REVERT: A 3030 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7079 (mmm) REVERT: A 3169 MET cc_start: 0.8289 (mmt) cc_final: 0.7237 (mmt) REVERT: A 3487 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5570 (pm20) REVERT: A 3551 GLU cc_start: 0.8046 (mp0) cc_final: 0.7648 (tt0) REVERT: A 3637 ASP cc_start: 0.7863 (m-30) cc_final: 0.7634 (m-30) REVERT: A 3715 GLU cc_start: 0.7629 (tp30) cc_final: 0.7407 (mm-30) REVERT: A 3732 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7203 (mt) REVERT: A 3741 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.4424 (ptp-170) REVERT: A 3786 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7416 (pt0) REVERT: A 3967 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6978 (pt0) REVERT: A 4071 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6776 (pt) REVERT: A 4129 GLU cc_start: 0.7485 (tp30) cc_final: 0.7258 (tp30) REVERT: A 4259 GLU cc_start: 0.7555 (pt0) cc_final: 0.7218 (tt0) REVERT: A 4283 LYS cc_start: 0.8018 (mttp) cc_final: 0.7504 (mtpt) REVERT: A 4301 ARG cc_start: 0.8219 (ptp-110) cc_final: 0.7803 (pmm-80) REVERT: A 4415 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6300 (ptm160) REVERT: A 4460 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.5906 (tt) REVERT: A 4502 LYS cc_start: 0.6366 (mmtm) cc_final: 0.5641 (mppt) outliers start: 72 outliers final: 41 residues processed: 336 average time/residue: 1.3697 time to fit residues: 542.8050 Evaluate side-chains 322 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1599 ARG Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2672 ASP Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2775 GLU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 224 optimal weight: 0.9990 chunk 192 optimal weight: 0.0030 chunk 231 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 274 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2588 HIS ** A3061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137740 restraints weight = 32791.520| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.29 r_work: 0.3558 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23578 Z= 0.118 Angle : 0.585 12.850 31985 Z= 0.287 Chirality : 0.040 0.226 3600 Planarity : 0.004 0.053 4087 Dihedral : 5.897 71.926 3193 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Rotamer: Outliers : 2.40 % Allowed : 18.50 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2841 helix: 1.93 (0.13), residues: 1605 sheet: -0.58 (0.35), residues: 229 loop : -0.55 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A3974 HIS 0.013 0.001 HIS A2588 PHE 0.036 0.001 PHE A4482 TYR 0.025 0.001 TYR A2748 ARG 0.007 0.000 ARG A1983 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 1316) hydrogen bonds : angle 3.98342 ( 3852) covalent geometry : bond 0.00261 (23578) covalent geometry : angle 0.58471 (31985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 1599 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7327 (tpp-160) REVERT: A 1792 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7249 (mt) REVERT: A 1819 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.8119 (tmm160) REVERT: A 1933 ASP cc_start: 0.6419 (m-30) cc_final: 0.5620 (p0) REVERT: A 1998 THR cc_start: 0.8120 (p) cc_final: 0.7881 (t) REVERT: A 2074 LYS cc_start: 0.8268 (tppt) cc_final: 0.7569 (ttmt) REVERT: A 2152 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7102 (pm20) REVERT: A 2315 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 2767 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7442 (mp0) REVERT: A 2779 MET cc_start: 0.8714 (mtp) cc_final: 0.8445 (mtp) REVERT: A 2858 PHE cc_start: 0.5266 (t80) cc_final: 0.4507 (t80) REVERT: A 2998 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (m-40) REVERT: A 3030 MET cc_start: 0.7403 (mmm) cc_final: 0.7199 (mmm) REVERT: A 3169 MET cc_start: 0.8268 (mmt) cc_final: 0.7246 (mmt) REVERT: A 3487 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5615 (pm20) REVERT: A 3551 GLU cc_start: 0.8069 (mp0) cc_final: 0.7631 (tt0) REVERT: A 3715 GLU cc_start: 0.7615 (tp30) cc_final: 0.7403 (mm-30) REVERT: A 3732 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7197 (mt) REVERT: A 3741 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.4341 (ptp-170) REVERT: A 3786 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7418 (pt0) REVERT: A 3967 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: A 4054 HIS cc_start: 0.6798 (m90) cc_final: 0.6567 (m-70) REVERT: A 4071 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6606 (pt) REVERT: A 4129 GLU cc_start: 0.7436 (tp30) cc_final: 0.6802 (tm-30) REVERT: A 4259 GLU cc_start: 0.7471 (pt0) cc_final: 0.7163 (tt0) REVERT: A 4276 ARG cc_start: 0.7498 (ppt170) cc_final: 0.7217 (pmt-80) REVERT: A 4283 LYS cc_start: 0.8017 (mttp) cc_final: 0.7504 (mtpt) REVERT: A 4301 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.7817 (pmm-80) REVERT: A 4311 LEU cc_start: 0.8445 (mm) cc_final: 0.8158 (mp) REVERT: A 4415 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6296 (ptm160) REVERT: A 4460 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.5999 (tt) REVERT: A 4502 LYS cc_start: 0.6356 (mmtm) cc_final: 0.5629 (mppt) outliers start: 61 outliers final: 33 residues processed: 336 average time/residue: 1.2358 time to fit residues: 488.2427 Evaluate side-chains 315 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1599 ARG Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4587 LEU Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 217 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 267 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 226 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1784 ASN A1860 GLN A1894 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2588 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136406 restraints weight = 32877.966| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.29 r_work: 0.3542 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23578 Z= 0.134 Angle : 0.601 14.067 31985 Z= 0.294 Chirality : 0.041 0.254 3600 Planarity : 0.004 0.053 4087 Dihedral : 5.915 71.708 3193 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.36 % Allowed : 19.02 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2841 helix: 1.90 (0.13), residues: 1603 sheet: -0.54 (0.35), residues: 229 loop : -0.55 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A2845 HIS 0.014 0.001 HIS A2588 PHE 0.035 0.002 PHE A4482 TYR 0.026 0.001 TYR A2748 ARG 0.006 0.000 ARG A1983 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1316) hydrogen bonds : angle 4.01397 ( 3852) covalent geometry : bond 0.00310 (23578) covalent geometry : angle 0.60140 (31985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 3.515 Fit side-chains revert: symmetry clash REVERT: A 1599 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7342 (tpp-160) REVERT: A 1792 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7280 (mt) REVERT: A 1819 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.8132 (tmm160) REVERT: A 1933 ASP cc_start: 0.6383 (m-30) cc_final: 0.5494 (p0) REVERT: A 1983 ARG cc_start: 0.6414 (ttt-90) cc_final: 0.6144 (ttt180) REVERT: A 1998 THR cc_start: 0.8129 (p) cc_final: 0.7895 (t) REVERT: A 2074 LYS cc_start: 0.8387 (tppt) cc_final: 0.7725 (ttmt) REVERT: A 2152 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7114 (pm20) REVERT: A 2315 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 2615 MET cc_start: 0.7837 (mmp) cc_final: 0.7361 (mmp) REVERT: A 2767 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7453 (mp0) REVERT: A 2779 MET cc_start: 0.8720 (mtp) cc_final: 0.8450 (mtp) REVERT: A 2858 PHE cc_start: 0.5261 (t80) cc_final: 0.4496 (t80) REVERT: A 2998 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7990 (m-40) REVERT: A 3169 MET cc_start: 0.8262 (mmt) cc_final: 0.7233 (mmt) REVERT: A 3487 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: A 3551 GLU cc_start: 0.8039 (mp0) cc_final: 0.7605 (tt0) REVERT: A 3601 MET cc_start: 0.8610 (mmm) cc_final: 0.8386 (mmp) REVERT: A 3649 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 3715 GLU cc_start: 0.7627 (tp30) cc_final: 0.7408 (mm-30) REVERT: A 3732 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7151 (mt) REVERT: A 3741 ARG cc_start: 0.5125 (OUTLIER) cc_final: 0.4350 (ptp-170) REVERT: A 3786 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7301 (pt0) REVERT: A 3967 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6987 (pt0) REVERT: A 4054 HIS cc_start: 0.6796 (m90) cc_final: 0.6550 (m-70) REVERT: A 4071 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6608 (pt) REVERT: A 4129 GLU cc_start: 0.7460 (tp30) cc_final: 0.7256 (tp30) REVERT: A 4259 GLU cc_start: 0.7479 (pt0) cc_final: 0.7176 (tt0) REVERT: A 4276 ARG cc_start: 0.7553 (ppt170) cc_final: 0.7258 (pmt-80) REVERT: A 4283 LYS cc_start: 0.8011 (mttp) cc_final: 0.7494 (mtpt) REVERT: A 4301 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.7838 (pmm-80) REVERT: A 4415 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6330 (ptm160) REVERT: A 4460 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6152 (tt) REVERT: A 4502 LYS cc_start: 0.6295 (mmtm) cc_final: 0.5573 (mppt) outliers start: 60 outliers final: 32 residues processed: 321 average time/residue: 1.8119 time to fit residues: 691.8323 Evaluate side-chains 308 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1599 ARG Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1792 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2985 CYS Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3487 GLU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3649 LEU Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3741 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3967 GLU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 237 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 102 optimal weight: 0.0270 chunk 284 optimal weight: 0.6980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN A1894 GLN A2271 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3852 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** 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 = 0.4024 r_free = 0.4024 target = 0.165153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133687 restraints weight = 32903.149| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.39 r_work: 0.3536 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23578 Z= 0.128 Angle : 0.601 13.679 31985 Z= 0.294 Chirality : 0.041 0.270 3600 Planarity : 0.004 0.052 4087 Dihedral : 5.881 71.685 3193 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 2.48 % Allowed : 19.09 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2841 helix: 1.89 (0.13), residues: 1608 sheet: -0.49 (0.34), residues: 227 loop : -0.51 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A2845 HIS 0.012 0.001 HIS A2588 PHE 0.036 0.001 PHE A4482 TYR 0.027 0.001 TYR A2748 ARG 0.011 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1316) hydrogen bonds : angle 4.00599 ( 3852) covalent geometry : bond 0.00292 (23578) covalent geometry : angle 0.60079 (31985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18226.36 seconds wall clock time: 316 minutes 29.44 seconds (18989.44 seconds total)