Starting phenix.real_space_refine on Sat Apr 13 05:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/04_2024/8pqy_17828_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 151 5.16 5 C 17748 2.51 5 N 4840 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 1525": "OD1" <-> "OD2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1980": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2775": "OE1" <-> "OE2" Residue "A PHE 2776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3100": "OE1" <-> "OE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3131": "OD1" <-> "OD2" Residue "A PHE 3823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 287": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22814 Classifications: {'peptide': 2892} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 4, 'PTRANS': 125, 'TRANS': 2762} Chain breaks: 13 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 330 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 14.95, per 1000 atoms: 0.54 Number of scatterers: 27916 At special positions: 0 Unit cell: (129.198, 140.847, 210.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 151 16.00 P 9 15.00 Mg 2 11.99 O 5166 8.00 N 4840 7.00 C 17748 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 - 3.50 Amino acid : False - 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: 10.27 Conformation dependent library (CDL) restraints added in 4.9 seconds 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 31 sheets defined 45.3% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.66 Creating SS restraints... Processing helix chain 'A' and resid 1445 through 1471 Processing helix chain 'A' and resid 1490 through 1509 removed outlier: 4.158A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1553 removed outlier: 4.014A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1584 Processing helix chain 'A' and resid 1588 through 1593 Processing helix chain 'A' and resid 1597 through 1615 Processing helix chain 'A' and resid 1617 through 1624 removed outlier: 3.964A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1634 through 1642 Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1654 through 1657 No H-bonds generated for 'chain 'A' and resid 1654 through 1657' Processing helix chain 'A' and resid 1692 through 1694 No H-bonds generated for 'chain 'A' and resid 1692 through 1694' Processing helix chain 'A' and resid 1698 through 1727 removed outlier: 3.521A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1747 through 1767 Processing helix chain 'A' and resid 1776 through 1796 Processing helix chain 'A' and resid 1802 through 1826 Processing helix chain 'A' and resid 1836 through 1839 No H-bonds generated for 'chain 'A' and resid 1836 through 1839' Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1883 through 1897 Processing helix chain 'A' and resid 1913 through 1922 Processing helix chain 'A' and resid 1938 through 1951 Processing helix chain 'A' and resid 1966 through 1985 removed outlier: 3.847A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2035 removed outlier: 3.586A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2030 through 2035' Processing helix chain 'A' and resid 2046 through 2057 Processing helix chain 'A' and resid 2062 through 2079 Proline residue: A2071 - end of helix removed outlier: 3.798A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2090 through 2113 removed outlier: 3.619A pdb=" N SER A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2145 Processing helix chain 'A' and resid 2154 through 2164 Processing helix chain 'A' and resid 2176 through 2188 Processing helix chain 'A' and resid 2201 through 2216 Processing helix chain 'A' and resid 2230 through 2245 Processing helix chain 'A' and resid 2261 through 2265 Processing helix chain 'A' and resid 2279 through 2289 Processing helix chain 'A' and resid 2312 through 2314 No H-bonds generated for 'chain 'A' and resid 2312 through 2314' Processing helix chain 'A' and resid 2353 through 2356 No H-bonds generated for 'chain 'A' and resid 2353 through 2356' Processing helix chain 'A' and resid 2371 through 2383 Processing helix chain 'A' and resid 2411 through 2427 Proline residue: A2425 - end of helix Processing helix chain 'A' and resid 2433 through 2442 removed outlier: 3.547A pdb=" N PHE A2441 " --> pdb=" O LEU A2437 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2475 Processing helix chain 'A' and resid 2483 through 2502 removed outlier: 4.209A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2521 Processing helix chain 'A' and resid 2534 through 2536 No H-bonds generated for 'chain 'A' and resid 2534 through 2536' Processing helix chain 'A' and resid 2548 through 2551 No H-bonds generated for 'chain 'A' and resid 2548 through 2551' Processing helix chain 'A' and resid 2572 through 2586 Processing helix chain 'A' and resid 2601 through 2611 removed outlier: 3.535A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2678 through 2688 Processing helix chain 'A' and resid 2725 through 2728 No H-bonds generated for 'chain 'A' and resid 2725 through 2728' Processing helix chain 'A' and resid 2741 through 2757 removed outlier: 5.001A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG A2757 " --> pdb=" O ARG A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2780 removed outlier: 4.920A pdb=" N GLU A2767 " --> pdb=" O THR A2764 " (cutoff:3.500A) Proline residue: A2768 - end of helix removed outlier: 4.846A pdb=" N PHE A2776 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2796 through 2810 Processing helix chain 'A' and resid 2818 through 2833 Processing helix chain 'A' and resid 2840 through 2857 Processing helix chain 'A' and resid 2863 through 2866 No H-bonds generated for 'chain 'A' and resid 2863 through 2866' Processing helix chain 'A' and resid 2886 through 2902 removed outlier: 4.283A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2927 Processing helix chain 'A' and resid 2943 through 2953 removed outlier: 3.549A pdb=" N SER A2947 " --> pdb=" O LYS A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2969 through 2984 Processing helix chain 'A' and resid 3002 through 3013 Processing helix chain 'A' and resid 3024 through 3040 Processing helix chain 'A' and resid 3048 through 3061 Processing helix chain 'A' and resid 3074 through 3081 removed outlier: 3.659A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3084 through 3087 No H-bonds generated for 'chain 'A' and resid 3084 through 3087' Processing helix chain 'A' and resid 3099 through 3109 Processing helix chain 'A' and resid 3139 through 3164 removed outlier: 3.711A pdb=" N ALA A3159 " --> pdb=" O HIS A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3173 through 3239 removed outlier: 3.692A pdb=" N ALA A3184 " --> pdb=" O ILE A3180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A3203 " --> pdb=" O MET A3199 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A3237 " --> pdb=" O ASN A3233 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3501 removed outlier: 4.009A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) Processing helix chain 'A' and resid 3503 through 3515 Processing helix chain 'A' and resid 3522 through 3538 Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3571 through 3581 Processing helix chain 'A' and resid 3595 through 3603 Processing helix chain 'A' and resid 3620 through 3629 Processing helix chain 'A' and resid 3643 through 3649 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3690 through 3695 removed outlier: 4.180A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3705 through 3720 Processing helix chain 'A' and resid 3722 through 3755 removed outlier: 3.825A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3765 through 3822 removed outlier: 4.208A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) Proline residue: A3803 - end of helix removed outlier: 4.500A pdb=" N LYS A3819 " --> pdb=" O MET A3815 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLN A3820 " --> pdb=" O GLU A3816 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE A3821 " --> pdb=" O SER A3817 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS A3822 " --> pdb=" O LEU A3818 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3840 Processing helix chain 'A' and resid 3852 through 3874 removed outlier: 3.996A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 4.813A pdb=" N ILE A3881 " --> pdb=" O GLN A3878 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A3882 " --> pdb=" O ASP A3879 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3909 Processing helix chain 'A' and resid 3929 through 3940 removed outlier: 4.144A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 3.776A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3996 Processing helix chain 'A' and resid 3998 through 4012 removed outlier: 3.561A pdb=" N LEU A4001 " --> pdb=" O PRO A3998 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A4002 " --> pdb=" O ASP A3999 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A4003 " --> pdb=" O ARG A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4052 through 4061 Processing helix chain 'A' and resid 4074 through 4089 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4103 through 4114 removed outlier: 4.371A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4141 Processing helix chain 'A' and resid 4153 through 4163 Processing helix chain 'A' and resid 4166 through 4169 No H-bonds generated for 'chain 'A' and resid 4166 through 4169' Processing helix chain 'A' and resid 4176 through 4192 Processing helix chain 'A' and resid 4209 through 4226 Processing helix chain 'A' and resid 4235 through 4237 No H-bonds generated for 'chain 'A' and resid 4235 through 4237' Processing helix chain 'A' and resid 4240 through 4249 Processing helix chain 'A' and resid 4259 through 4272 Processing helix chain 'A' and resid 4275 through 4278 No H-bonds generated for 'chain 'A' and resid 4275 through 4278' Processing helix chain 'A' and resid 4302 through 4309 Processing helix chain 'A' and resid 4318 through 4321 Processing helix chain 'A' and resid 4329 through 4346 removed outlier: 3.600A pdb=" N LYS A4345 " --> pdb=" O SER A4341 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4394 Proline residue: A4392 - end of helix Processing helix chain 'A' and resid 4408 through 4438 Processing helix chain 'A' and resid 4446 through 4457 Processing helix chain 'A' and resid 4475 through 4496 removed outlier: 3.647A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4504 through 4506 No H-bonds generated for 'chain 'A' and resid 4504 through 4506' Processing helix chain 'A' and resid 4511 through 4513 No H-bonds generated for 'chain 'A' and resid 4511 through 4513' Processing helix chain 'A' and resid 4517 through 4532 Processing helix chain 'A' and resid 4536 through 4538 No H-bonds generated for 'chain 'A' and resid 4536 through 4538' Processing helix chain 'A' and resid 4632 through 4637 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.062A pdb=" N SER B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.876A pdb=" N SER C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.540A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 6.541A pdb=" N ILE A1665 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE A1676 " --> pdb=" O SER A1663 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id= D, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id= E, first strand: chain 'A' and resid 1954 through 1958 removed outlier: 6.604A pdb=" N ALA A2013 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE A1957 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE A2015 " --> pdb=" O PHE A1957 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id= G, first strand: chain 'A' and resid 2360 through 2364 removed outlier: 8.897A pdb=" N LEU A2220 " --> pdb=" O VAL A2339 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A2341 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET A2222 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A2343 " --> pdb=" O MET A2222 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLY A2224 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id= I, first strand: chain 'A' and resid 2732 through 2735 removed outlier: 3.756A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.097A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3090 through 3093 removed outlier: 6.478A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 3697 through 3700 removed outlier: 7.440A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id= N, first strand: chain 'A' and resid 4143 through 4147 removed outlier: 6.534A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 6.968A pdb=" N GLY A4559 " --> pdb=" O VAL A4509 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 4568 through 4570 Processing sheet with id= Q, first strand: chain 'A' and resid 4604 through 4610 removed outlier: 3.877A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.585A pdb=" N THR B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 399 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.910A pdb=" N ALA B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL B 114 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 124 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.988A pdb=" N CYS B 168 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 156 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 166 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 158 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 164 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 169 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 186 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP B 178 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N CYS B 184 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.724A pdb=" N LYS B 228 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 237 through 242 removed outlier: 7.035A pdb=" N CYS B 252 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B 240 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA B 250 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 248 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 262 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS B 268 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.892A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 332 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 341 through 346 removed outlier: 6.809A pdb=" N CYS B 356 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL B 344 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 354 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE B 346 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE B 352 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 102 through 105 removed outlier: 4.891A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 399 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.914A pdb=" N ALA C 126 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL C 114 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 124 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP C 136 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE C 142 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 155 through 157 removed outlier: 3.820A pdb=" N ASP C 155 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.721A pdb=" N ALA C 210 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 198 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 208 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE C 200 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS C 206 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 211 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.981A pdb=" N CYS C 252 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL C 240 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 250 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU C 248 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 262 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS C 268 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.750A pdb=" N GLY C 314 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE C 282 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 312 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP C 284 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE C 310 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 332 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 346 removed outlier: 6.851A pdb=" N CYS C 356 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL C 344 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C 354 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C 346 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 352 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 357 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3762 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: 18.97 Time building geometry restraints manager: 11.21 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: 9075 1.34 - 1.46: 6496 1.46 - 1.59: 12697 1.59 - 1.71: 13 1.71 - 1.83: 245 Bond restraints: 28526 Sorted by residual: bond pdb=" C ARG A2869 " pdb=" N PRO A2870 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" CB PRO A3643 " pdb=" CG PRO A3643 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.42e+00 bond pdb=" CA GLU A1567 " pdb=" C GLU A1567 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.27e-02 6.20e+03 6.31e+00 bond pdb=" CA GLU A1610 " pdb=" C GLU A1610 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.24e-02 6.50e+03 5.50e+00 bond pdb=" CB PRO A2817 " pdb=" CG PRO A2817 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.36e+00 ... (remaining 28521 not shown) Histogram of bond angle deviations from ideal: 94.93 - 103.85: 411 103.85 - 112.78: 15481 112.78 - 121.71: 16472 121.71 - 130.64: 6182 130.64 - 139.56: 183 Bond angle restraints: 38729 Sorted by residual: angle pdb=" CA PRO A3643 " pdb=" N PRO A3643 " pdb=" CD PRO A3643 " ideal model delta sigma weight residual 112.00 94.93 17.07 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CG ARG A2729 " pdb=" CD ARG A2729 " pdb=" NE ARG A2729 " ideal model delta sigma weight residual 112.00 126.62 -14.62 2.20e+00 2.07e-01 4.42e+01 angle pdb=" CA PRO A2817 " pdb=" N PRO A2817 " pdb=" CD PRO A2817 " ideal model delta sigma weight residual 112.00 103.34 8.66 1.40e+00 5.10e-01 3.83e+01 angle pdb=" N ILE A1557 " pdb=" CA ILE A1557 " pdb=" C ILE A1557 " ideal model delta sigma weight residual 111.81 106.79 5.02 8.60e-01 1.35e+00 3.41e+01 angle pdb=" CB MET A1531 " pdb=" CG MET A1531 " pdb=" SD MET A1531 " ideal model delta sigma weight residual 112.70 129.34 -16.64 3.00e+00 1.11e-01 3.08e+01 ... (remaining 38724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 16067 28.38 - 56.77: 1029 56.77 - 85.15: 69 85.15 - 113.54: 5 113.54 - 141.92: 3 Dihedral angle restraints: 17173 sinusoidal: 6889 harmonic: 10284 Sorted by residual: dihedral pdb=" CA LEU A1963 " pdb=" C LEU A1963 " pdb=" N GLU A1964 " pdb=" CA GLU A1964 " ideal model delta harmonic sigma weight residual 180.00 143.22 36.78 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" O2A ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PA ADP A4806 " pdb=" PB ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 81.93 -141.92 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PB ADP A4806 " pdb=" PA ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 81.34 -141.35 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 17170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3680 0.065 - 0.129: 635 0.129 - 0.194: 75 0.194 - 0.258: 3 0.258 - 0.323: 5 Chirality restraints: 4398 Sorted by residual: chirality pdb=" CB VAL B 122 " pdb=" CA VAL B 122 " pdb=" CG1 VAL B 122 " pdb=" CG2 VAL B 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL A2557 " pdb=" CA VAL A2557 " pdb=" CG1 VAL A2557 " pdb=" CG2 VAL A2557 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A3745 " pdb=" CB LEU A3745 " pdb=" CD1 LEU A3745 " pdb=" CD2 LEU A3745 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4395 not shown) Planarity restraints: 4930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3642 " 0.129 5.00e-02 4.00e+02 1.79e-01 5.15e+01 pdb=" N PRO A3643 " -0.310 5.00e-02 4.00e+02 pdb=" CA PRO A3643 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO A3643 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A2928 " 0.057 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A2929 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A2929 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A2929 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3109 " -0.016 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A3109 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A3109 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A3109 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A3109 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3109 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A3109 " -0.001 2.00e-02 2.50e+03 ... (remaining 4927 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 170 2.50 - 3.10: 18151 3.10 - 3.70: 45526 3.70 - 4.30: 63340 4.30 - 4.90: 103205 Nonbonded interactions: 230392 Sorted by model distance: nonbonded pdb=" NH2 ARG A2729 " pdb="MG MG A4804 " model vdw 1.902 2.250 nonbonded pdb=" OG SER A2231 " pdb=" O2B ATP A4803 " model vdw 1.971 2.440 nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4802 " model vdw 1.981 2.170 nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 2.012 2.440 nonbonded pdb=" OD2 ASP A1958 " pdb="MG MG A4802 " model vdw 2.066 2.170 ... (remaining 230387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.480 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 84.850 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 0.153 28526 Z= 0.261 Angle : 0.892 17.074 38729 Z= 0.452 Chirality : 0.050 0.323 4398 Planarity : 0.007 0.179 4930 Dihedral : 17.214 141.924 10477 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 0.36 % Allowed : 22.29 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.91 (0.12), residues: 3482 helix: -1.08 (0.11), residues: 1650 sheet: -0.78 (0.22), residues: 491 loop : -1.48 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 261 HIS 0.006 0.001 HIS A2730 PHE 0.056 0.002 PHE A3109 TYR 0.033 0.002 TYR C 225 ARG 0.011 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9119 (tpp-160) cc_final: 0.8900 (tpp80) REVERT: A 2762 LEU cc_start: 0.7126 (mt) cc_final: 0.6818 (mp) REVERT: A 3500 MET cc_start: 0.8112 (tmm) cc_final: 0.7685 (tmm) REVERT: A 3924 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6090 (mm) REVERT: B 201 MET cc_start: 0.4875 (pmm) cc_final: 0.4674 (pmm) outliers start: 11 outliers final: 2 residues processed: 181 average time/residue: 0.4711 time to fit residues: 136.2563 Evaluate side-chains 162 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1610 GLU Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain C residue 290 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 7.9990 chunk 266 optimal weight: 0.0060 chunk 147 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1979 GLN ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2730 HIS A3735 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 GLN A4389 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28526 Z= 0.178 Angle : 0.553 11.291 38729 Z= 0.276 Chirality : 0.040 0.143 4398 Planarity : 0.005 0.096 4930 Dihedral : 6.746 143.509 3862 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.79 % Allowed : 22.19 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: -0.58 (0.14), residues: 3482 helix: 0.40 (0.12), residues: 1656 sheet: -0.62 (0.22), residues: 504 loop : -1.19 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 261 HIS 0.005 0.001 HIS A2588 PHE 0.015 0.001 PHE A3823 TYR 0.020 0.001 TYR A3836 ARG 0.007 0.000 ARG A2729 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9153 (tpp-160) cc_final: 0.8917 (tpt-90) REVERT: A 1879 LEU cc_start: 0.8065 (tp) cc_final: 0.7786 (tp) REVERT: A 1892 MET cc_start: 0.7837 (mmt) cc_final: 0.7463 (mmt) REVERT: A 2358 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6298 (ttp-110) REVERT: A 2487 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 2615 MET cc_start: 0.7718 (mmm) cc_final: 0.7417 (mmm) REVERT: A 3043 MET cc_start: 0.5364 (mmm) cc_final: 0.5011 (mmt) REVERT: A 3199 MET cc_start: 0.7701 (mmm) cc_final: 0.7360 (tpt) REVERT: A 3875 MET cc_start: 0.8476 (tpp) cc_final: 0.7973 (ttm) REVERT: C 322 MET cc_start: 0.7768 (tpp) cc_final: 0.7481 (tpp) outliers start: 54 outliers final: 23 residues processed: 209 average time/residue: 0.5029 time to fit residues: 167.5702 Evaluate side-chains 182 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 344 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 316 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 ASN A2134 GLN ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS A2964 HIS ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4006 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS B 381 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28526 Z= 0.281 Angle : 0.616 13.235 38729 Z= 0.307 Chirality : 0.042 0.271 4398 Planarity : 0.004 0.060 4930 Dihedral : 6.503 137.286 3855 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 4.07 % Allowed : 22.46 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: -0.26 (0.14), residues: 3482 helix: 0.83 (0.12), residues: 1665 sheet: -0.80 (0.22), residues: 516 loop : -1.13 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 261 HIS 0.005 0.001 HIS A2791 PHE 0.018 0.002 PHE A2912 TYR 0.022 0.002 TYR A3836 ARG 0.005 0.000 ARG A3474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 158 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9193 (tpp-160) cc_final: 0.8905 (tpt-90) REVERT: A 1892 MET cc_start: 0.7999 (mmt) cc_final: 0.7729 (mmt) REVERT: A 1960 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7588 (t80) REVERT: A 2189 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7581 (ttm) REVERT: A 2358 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6900 (ttp-170) REVERT: A 2538 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: A 3008 MET cc_start: 0.8438 (mmm) cc_final: 0.8056 (mmm) REVERT: A 3199 MET cc_start: 0.7564 (mmm) cc_final: 0.7311 (tpt) REVERT: A 3653 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8816 (p) REVERT: A 3747 LYS cc_start: 0.9183 (tmtt) cc_final: 0.8880 (mmtt) REVERT: A 3825 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6201 (p90) REVERT: A 3836 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 3875 MET cc_start: 0.8591 (tpp) cc_final: 0.8087 (ttm) REVERT: B 218 MET cc_start: 0.7243 (tpp) cc_final: 0.6937 (tpp) REVERT: B 261 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.5091 (m100) REVERT: C 311 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7270 (tt) outliers start: 123 outliers final: 62 residues processed: 269 average time/residue: 0.4151 time to fit residues: 183.2095 Evaluate side-chains 222 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 151 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2078 GLU Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3823 PHE Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 30.0000 chunk 240 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 152 optimal weight: 0.0470 chunk 214 optimal weight: 5.9990 chunk 320 optimal weight: 0.6980 chunk 339 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1595 GLN A1755 GLN A1921 HIS ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28526 Z= 0.138 Angle : 0.519 13.730 38729 Z= 0.256 Chirality : 0.040 0.141 4398 Planarity : 0.004 0.052 4930 Dihedral : 6.188 137.391 3855 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 24.38 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.21 (0.14), residues: 3482 helix: 1.33 (0.13), residues: 1669 sheet: -0.64 (0.23), residues: 483 loop : -1.06 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.003 0.001 HIS A1500 PHE 0.013 0.001 PHE A3823 TYR 0.019 0.001 TYR A3836 ARG 0.009 0.000 ARG A3997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 163 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8904 (tpt-90) REVERT: A 2189 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7505 (ttm) REVERT: A 2358 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6537 (ttp-170) REVERT: A 2461 MET cc_start: 0.8418 (mmm) cc_final: 0.8014 (mmm) REVERT: A 2487 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 2538 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: A 3008 MET cc_start: 0.8136 (mmm) cc_final: 0.7857 (mmm) REVERT: A 3155 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7608 (t-90) REVERT: A 3199 MET cc_start: 0.7531 (mmm) cc_final: 0.7301 (tpt) REVERT: A 3473 ASN cc_start: 0.9100 (m-40) cc_final: 0.8784 (p0) REVERT: A 3836 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 3875 MET cc_start: 0.8613 (tpp) cc_final: 0.8086 (ttm) REVERT: A 4296 MET cc_start: 0.7734 (tpt) cc_final: 0.7291 (tmm) REVERT: A 4419 MET cc_start: 0.7780 (tpp) cc_final: 0.7557 (tpp) REVERT: B 218 MET cc_start: 0.7205 (tpp) cc_final: 0.6885 (tpp) REVERT: B 261 TRP cc_start: 0.6662 (OUTLIER) cc_final: 0.5243 (m100) REVERT: B 332 MET cc_start: 0.5929 (tmm) cc_final: 0.5595 (tmm) REVERT: C 201 MET cc_start: 0.7353 (mpp) cc_final: 0.7083 (mpp) REVERT: C 322 MET cc_start: 0.7645 (tpp) cc_final: 0.7294 (tpp) REVERT: C 391 THR cc_start: 0.7763 (t) cc_final: 0.7533 (m) outliers start: 63 outliers final: 27 residues processed: 220 average time/residue: 0.4135 time to fit residues: 150.0819 Evaluate side-chains 184 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 289 optimal weight: 0.5980 chunk 234 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 173 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28526 Z= 0.178 Angle : 0.531 13.851 38729 Z= 0.262 Chirality : 0.040 0.142 4398 Planarity : 0.004 0.051 4930 Dihedral : 6.105 137.942 3855 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 3.15 % Allowed : 23.75 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.36 (0.14), residues: 3482 helix: 1.47 (0.13), residues: 1672 sheet: -0.70 (0.22), residues: 516 loop : -0.95 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 135 HIS 0.003 0.001 HIS A3852 PHE 0.015 0.001 PHE A3109 TYR 0.018 0.001 TYR A3836 ARG 0.012 0.000 ARG A3223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 159 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9197 (tpp-160) cc_final: 0.8911 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 1982 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 2189 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7582 (ttm) REVERT: A 2358 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6927 (ttp-170) REVERT: A 2461 MET cc_start: 0.8367 (mmm) cc_final: 0.7921 (mmm) REVERT: A 2538 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 2728 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6432 (pp) REVERT: A 3008 MET cc_start: 0.8177 (mmm) cc_final: 0.7943 (mmm) REVERT: A 3199 MET cc_start: 0.7513 (mmm) cc_final: 0.7298 (tpt) REVERT: A 3473 ASN cc_start: 0.9101 (m-40) cc_final: 0.8774 (p0) REVERT: A 3836 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7829 (t80) REVERT: A 3875 MET cc_start: 0.8635 (tpp) cc_final: 0.8105 (ttm) REVERT: A 3999 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7195 (p0) REVERT: B 261 TRP cc_start: 0.6566 (OUTLIER) cc_final: 0.4998 (m100) REVERT: B 332 MET cc_start: 0.5970 (tmm) cc_final: 0.5567 (tmm) REVERT: C 164 LEU cc_start: 0.8420 (tp) cc_final: 0.7922 (tt) REVERT: C 201 MET cc_start: 0.7558 (mpp) cc_final: 0.7335 (mpp) REVERT: C 322 MET cc_start: 0.7643 (tpp) cc_final: 0.7286 (tpp) outliers start: 95 outliers final: 63 residues processed: 248 average time/residue: 0.4135 time to fit residues: 167.8102 Evaluate side-chains 226 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 154 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2079 GLN Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 5.9990 chunk 305 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 199 optimal weight: 0.0020 chunk 83 optimal weight: 0.9990 chunk 339 optimal weight: 0.7980 chunk 281 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28526 Z= 0.186 Angle : 0.537 14.019 38729 Z= 0.265 Chirality : 0.040 0.296 4398 Planarity : 0.004 0.050 4930 Dihedral : 6.072 138.832 3855 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.41 % Allowed : 23.88 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.42 (0.14), residues: 3482 helix: 1.55 (0.13), residues: 1671 sheet: -0.69 (0.22), residues: 516 loop : -0.94 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.007 0.001 HIS A2857 PHE 0.017 0.001 PHE A3109 TYR 0.018 0.001 TYR A1546 ARG 0.007 0.000 ARG A3223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 160 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9210 (tpp-160) cc_final: 0.8937 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7378 (t80) REVERT: A 1982 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7366 (mm) REVERT: A 2189 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7593 (ttm) REVERT: A 2487 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 2538 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: A 2545 TRP cc_start: 0.6535 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: A 3008 MET cc_start: 0.8211 (mmm) cc_final: 0.7943 (mmm) REVERT: A 3068 MET cc_start: 0.7496 (ptp) cc_final: 0.7241 (ptp) REVERT: A 3199 MET cc_start: 0.7486 (mmm) cc_final: 0.7246 (tpt) REVERT: A 3473 ASN cc_start: 0.9067 (m-40) cc_final: 0.8764 (p0) REVERT: A 3747 LYS cc_start: 0.9235 (tmtt) cc_final: 0.8905 (mmtt) REVERT: A 3836 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 3875 MET cc_start: 0.8665 (tpp) cc_final: 0.8062 (ttm) REVERT: A 4455 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7541 (mm) REVERT: B 218 MET cc_start: 0.7273 (tpp) cc_final: 0.6752 (tpp) REVERT: B 261 TRP cc_start: 0.6569 (OUTLIER) cc_final: 0.4959 (m100) REVERT: B 332 MET cc_start: 0.5958 (tmm) cc_final: 0.5571 (tmm) REVERT: C 164 LEU cc_start: 0.8521 (tp) cc_final: 0.8044 (tt) REVERT: C 322 MET cc_start: 0.7647 (tpp) cc_final: 0.7298 (tpp) outliers start: 103 outliers final: 71 residues processed: 255 average time/residue: 0.4372 time to fit residues: 187.7740 Evaluate side-chains 234 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 155 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2079 GLN Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 285 optimal weight: 20.0000 chunk 189 optimal weight: 0.0870 chunk 338 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2707 GLN A3175 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28526 Z= 0.168 Angle : 0.534 14.048 38729 Z= 0.262 Chirality : 0.040 0.226 4398 Planarity : 0.003 0.050 4930 Dihedral : 6.015 139.520 3855 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.41 % Allowed : 24.01 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.50 (0.14), residues: 3482 helix: 1.64 (0.13), residues: 1671 sheet: -0.66 (0.22), residues: 510 loop : -0.94 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.004 0.001 HIS A3155 PHE 0.019 0.001 PHE A3109 TYR 0.024 0.001 TYR A3026 ARG 0.010 0.000 ARG A3223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 158 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9217 (tpp-160) cc_final: 0.8981 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7368 (t80) REVERT: A 1982 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7335 (mm) REVERT: A 2189 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7537 (ttm) REVERT: A 2461 MET cc_start: 0.8415 (mmm) cc_final: 0.8009 (mmm) REVERT: A 2487 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 2538 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: A 2545 TRP cc_start: 0.6524 (OUTLIER) cc_final: 0.6293 (m-10) REVERT: A 3008 MET cc_start: 0.8195 (mmm) cc_final: 0.7924 (mmm) REVERT: A 3068 MET cc_start: 0.7572 (ptp) cc_final: 0.7348 (ptp) REVERT: A 3199 MET cc_start: 0.7402 (mmm) cc_final: 0.7147 (tpt) REVERT: A 3473 ASN cc_start: 0.9096 (m-40) cc_final: 0.8765 (p0) REVERT: A 3836 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7836 (t80) REVERT: A 3875 MET cc_start: 0.8668 (tpp) cc_final: 0.8082 (ttm) REVERT: A 3999 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7164 (p0) REVERT: A 4455 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 218 MET cc_start: 0.7345 (tpp) cc_final: 0.6998 (tpp) REVERT: B 261 TRP cc_start: 0.6621 (OUTLIER) cc_final: 0.5111 (m100) REVERT: B 332 MET cc_start: 0.6029 (tmm) cc_final: 0.5727 (tmm) REVERT: C 164 LEU cc_start: 0.8557 (tp) cc_final: 0.8084 (tt) REVERT: C 201 MET cc_start: 0.7551 (mpp) cc_final: 0.7287 (mpp) REVERT: C 322 MET cc_start: 0.7630 (tpp) cc_final: 0.7276 (tpp) outliers start: 103 outliers final: 77 residues processed: 251 average time/residue: 0.4223 time to fit residues: 174.0140 Evaluate side-chains 241 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 155 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2660 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 202 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 265 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28526 Z= 0.149 Angle : 0.525 14.027 38729 Z= 0.257 Chirality : 0.040 0.202 4398 Planarity : 0.003 0.050 4930 Dihedral : 5.940 140.027 3855 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 3.11 % Allowed : 24.35 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.60 (0.14), residues: 3482 helix: 1.74 (0.13), residues: 1677 sheet: -0.63 (0.22), residues: 500 loop : -0.92 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.004 0.001 HIS A2857 PHE 0.023 0.001 PHE A3109 TYR 0.016 0.001 TYR A1546 ARG 0.010 0.000 ARG A3223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 163 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9238 (tpp-160) cc_final: 0.8992 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 1982 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7451 (mm) REVERT: A 2189 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: A 2461 MET cc_start: 0.8353 (mmm) cc_final: 0.7900 (mmm) REVERT: A 2538 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: A 2545 TRP cc_start: 0.6534 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: A 2671 MET cc_start: 0.7919 (tmm) cc_final: 0.7690 (tmm) REVERT: A 3008 MET cc_start: 0.8164 (mmm) cc_final: 0.7897 (mmm) REVERT: A 3068 MET cc_start: 0.7537 (ptp) cc_final: 0.7324 (ptp) REVERT: A 3199 MET cc_start: 0.7345 (mmm) cc_final: 0.7094 (tpt) REVERT: A 3875 MET cc_start: 0.8645 (tpp) cc_final: 0.8050 (ttm) REVERT: A 4455 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7490 (mm) REVERT: B 261 TRP cc_start: 0.6584 (OUTLIER) cc_final: 0.5094 (m100) REVERT: B 332 MET cc_start: 0.5986 (tmm) cc_final: 0.5698 (tmm) REVERT: C 164 LEU cc_start: 0.8574 (tp) cc_final: 0.8070 (tt) REVERT: C 201 MET cc_start: 0.7456 (mpp) cc_final: 0.7218 (mpp) REVERT: C 322 MET cc_start: 0.7575 (tpp) cc_final: 0.6890 (tpp) outliers start: 94 outliers final: 75 residues processed: 247 average time/residue: 0.4265 time to fit residues: 172.3017 Evaluate side-chains 240 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 158 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2199 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2660 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 4.9990 chunk 324 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 137 optimal weight: 0.4980 chunk 247 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 298 optimal weight: 0.7980 chunk 314 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28526 Z= 0.201 Angle : 0.558 14.009 38729 Z= 0.274 Chirality : 0.040 0.200 4398 Planarity : 0.004 0.050 4930 Dihedral : 5.974 141.084 3855 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 3.41 % Allowed : 24.18 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.54 (0.14), residues: 3482 helix: 1.69 (0.13), residues: 1672 sheet: -0.67 (0.22), residues: 522 loop : -0.95 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.004 0.001 HIS A2445 PHE 0.024 0.001 PHE A3109 TYR 0.016 0.001 TYR A3836 ARG 0.009 0.000 ARG A2643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 163 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9245 (tpp-160) cc_final: 0.9013 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7326 (t80) REVERT: A 1982 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7421 (mm) REVERT: A 2073 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5549 (m-10) REVERT: A 2189 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7543 (ttm) REVERT: A 2538 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: A 2545 TRP cc_start: 0.6589 (OUTLIER) cc_final: 0.6340 (m-10) REVERT: A 3008 MET cc_start: 0.8220 (mmm) cc_final: 0.7941 (mmm) REVERT: A 3199 MET cc_start: 0.7356 (mmm) cc_final: 0.7123 (tpt) REVERT: A 3875 MET cc_start: 0.8701 (tpp) cc_final: 0.8106 (ttm) REVERT: A 4455 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7523 (mm) REVERT: B 218 MET cc_start: 0.7266 (tpp) cc_final: 0.6876 (tpp) REVERT: B 239 MET cc_start: 0.7871 (ppp) cc_final: 0.7636 (ppp) REVERT: B 261 TRP cc_start: 0.6604 (OUTLIER) cc_final: 0.4986 (m100) REVERT: B 332 MET cc_start: 0.6418 (tmm) cc_final: 0.6075 (tmm) REVERT: C 164 LEU cc_start: 0.8604 (tp) cc_final: 0.8212 (tt) REVERT: C 311 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6720 (tt) REVERT: C 322 MET cc_start: 0.7639 (tpp) cc_final: 0.6919 (tpp) outliers start: 103 outliers final: 84 residues processed: 257 average time/residue: 0.4366 time to fit residues: 184.6744 Evaluate side-chains 250 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 157 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 231 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3878 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4335 GLN A4389 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28526 Z= 0.230 Angle : 0.594 14.318 38729 Z= 0.291 Chirality : 0.041 0.200 4398 Planarity : 0.004 0.051 4930 Dihedral : 6.024 142.354 3855 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 3.18 % Allowed : 24.51 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.40 (0.14), residues: 3482 helix: 1.60 (0.13), residues: 1669 sheet: -0.76 (0.22), residues: 522 loop : -1.02 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 323 HIS 0.004 0.001 HIS B 337 PHE 0.017 0.001 PHE A3109 TYR 0.027 0.001 TYR A3026 ARG 0.012 0.000 ARG A3223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 160 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1960 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 1982 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7501 (mm) REVERT: A 2073 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5677 (m-10) REVERT: A 2189 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7559 (ttm) REVERT: A 2538 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: A 2960 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7415 (tt0) REVERT: A 3008 MET cc_start: 0.8261 (mmm) cc_final: 0.7976 (mmm) REVERT: A 3875 MET cc_start: 0.8752 (tpp) cc_final: 0.8204 (ttm) REVERT: B 218 MET cc_start: 0.7369 (tpp) cc_final: 0.7020 (tpp) REVERT: B 261 TRP cc_start: 0.6675 (OUTLIER) cc_final: 0.5053 (m100) REVERT: B 332 MET cc_start: 0.6384 (tmm) cc_final: 0.6038 (tmm) REVERT: C 164 LEU cc_start: 0.8575 (tp) cc_final: 0.8082 (tt) REVERT: C 311 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7208 (tt) REVERT: C 322 MET cc_start: 0.7619 (tpp) cc_final: 0.7239 (tpp) outliers start: 96 outliers final: 80 residues processed: 246 average time/residue: 0.4239 time to fit residues: 171.9185 Evaluate side-chains 242 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 155 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2707 GLN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.057843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.050097 restraints weight = 187701.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.051181 restraints weight = 106859.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.051942 restraints weight = 72300.226| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28526 Z= 0.179 Angle : 0.569 14.424 38729 Z= 0.277 Chirality : 0.041 0.197 4398 Planarity : 0.003 0.051 4930 Dihedral : 5.926 141.386 3855 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.95 % Allowed : 24.71 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.56 (0.14), residues: 3482 helix: 1.75 (0.13), residues: 1663 sheet: -0.75 (0.22), residues: 518 loop : -0.94 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2545 HIS 0.005 0.001 HIS A2857 PHE 0.016 0.001 PHE A3109 TYR 0.022 0.001 TYR C 225 ARG 0.010 0.000 ARG A3223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.61 seconds wall clock time: 95 minutes 17.49 seconds (5717.49 seconds total)