Starting phenix.real_space_refine on Sat Mar 23 02:13:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/03_2024/6tax_10429_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 207 5.16 5 C 22436 2.51 5 N 6060 2.21 5 O 6526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2507": "NH1" <-> "NH2" Residue "A ARG 2523": "NH1" <-> "NH2" Residue "A TYR 2837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4926": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35235 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 35235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4420, 35235 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'peptide': 4416, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 181, 'TRANS': 4234, None: 4} Not linked: pdbres="GLY A5150 " pdbres="ATP A5201 " Not linked: pdbres="ATP A5201 " pdbres=" MG A5202 " Not linked: pdbres=" MG A5202 " pdbres=" ZN A5203 " Not linked: pdbres=" ZN A5203 " pdbres=" ZN A5204 " Chain breaks: 15 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'UNK:plan-1': 67, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26222 SG CYS A3962 90.097 130.185 218.776 1.00165.01 S ATOM 26386 SG CYS A3982 86.969 128.250 221.967 1.00171.20 S ATOM 26411 SG CYS A3985 90.556 128.936 222.124 1.00173.12 S ATOM 26112 SG CYS A3947 80.309 123.526 217.441 0.50141.40 S ATOM 26137 SG CYS A3950 77.879 120.194 215.933 1.00139.88 S ATOM 26265 SG CYS A3967 77.339 123.186 214.009 1.00159.05 S ATOM 26290 SG CYS A3970 75.799 123.843 217.598 1.00161.62 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A3947 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A3947 " occ=0.50 Time building chain proxies: 18.51, per 1000 atoms: 0.53 Number of scatterers: 35235 At special positions: 0 Unit cell: (128.96, 150.8, 242.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 207 16.00 P 3 15.00 Mg 1 11.99 O 6526 8.00 N 6060 7.00 C 22436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.03 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: 13.58 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 13 sheets defined 53.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 22.55 Creating SS restraints... Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 522 through 539 Processing helix chain 'A' and resid 593 through 604 removed outlier: 4.740A pdb=" N ALA A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 614 through 617 No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 629 through 639 Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 644 through 657 removed outlier: 3.563A pdb=" N CYS A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 657 " --> pdb=" O CYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 666 Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 760 through 774 Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 781 through 800 Processing helix chain 'A' and resid 811 through 826 Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.905A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 888 removed outlier: 3.545A pdb=" N SER A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 917 Processing helix chain 'A' and resid 930 through 938 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 963 through 981 Processing helix chain 'A' and resid 995 through 1009 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1032 through 1043 removed outlier: 3.796A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1048 No H-bonds generated for 'chain 'A' and resid 1045 through 1048' Processing helix chain 'A' and resid 1054 through 1071 Processing helix chain 'A' and resid 1080 through 1088 Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1155 through 1158 No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1167 through 1170 Processing helix chain 'A' and resid 1191 through 1202 Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1234 through 1240 removed outlier: 3.753A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1263 through 1269 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1299 through 1328 Processing helix chain 'A' and resid 1339 through 1345 Processing helix chain 'A' and resid 1362 through 1367 removed outlier: 4.074A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1404 through 1414 removed outlier: 3.919A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1439 removed outlier: 4.644A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1463 removed outlier: 3.848A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 4.114A pdb=" N ASN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A1479 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1506 Processing helix chain 'A' and resid 1522 through 1525 No H-bonds generated for 'chain 'A' and resid 1522 through 1525' Processing helix chain 'A' and resid 1545 through 1556 Processing helix chain 'A' and resid 1564 through 1593 Processing helix chain 'A' and resid 1631 through 1659 removed outlier: 3.637A pdb=" N GLU A1659 " --> pdb=" O GLN A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1665 Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1700 through 1708 Processing helix chain 'A' and resid 1714 through 1725 Processing helix chain 'A' and resid 1727 through 1730 No H-bonds generated for 'chain 'A' and resid 1727 through 1730' Processing helix chain 'A' and resid 1736 through 1749 Processing helix chain 'A' and resid 1761 through 1774 removed outlier: 3.594A pdb=" N THR A1773 " --> pdb=" O ALA A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1801 No H-bonds generated for 'chain 'A' and resid 1799 through 1801' Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.726A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1843 Processing helix chain 'A' and resid 1859 through 1861 No H-bonds generated for 'chain 'A' and resid 1859 through 1861' Processing helix chain 'A' and resid 1864 through 1880 Processing helix chain 'A' and resid 1901 through 1904 No H-bonds generated for 'chain 'A' and resid 1901 through 1904' Processing helix chain 'A' and resid 1906 through 1908 No H-bonds generated for 'chain 'A' and resid 1906 through 1908' Processing helix chain 'A' and resid 1918 through 1929 Processing helix chain 'A' and resid 1938 through 1941 removed outlier: 3.644A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1938 through 1941' Processing helix chain 'A' and resid 1960 through 1973 Processing helix chain 'A' and resid 1994 through 2002 Processing helix chain 'A' and resid 2028 through 2036 Processing helix chain 'A' and resid 2081 through 2087 removed outlier: 3.990A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A2087 " --> pdb=" O LYS A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2120 No H-bonds generated for 'chain 'A' and resid 2117 through 2120' Processing helix chain 'A' and resid 2123 through 2136 Proline residue: A2128 - end of helix removed outlier: 4.080A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2165 Processing helix chain 'A' and resid 2173 through 2192 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2208 through 2223 Processing helix chain 'A' and resid 2309 through 2317 Processing helix chain 'A' and resid 2331 through 2341 Processing helix chain 'A' and resid 2358 through 2373 Processing helix chain 'A' and resid 2388 through 2399 Processing helix chain 'A' and resid 2418 through 2439 Processing helix chain 'A' and resid 2454 through 2463 removed outlier: 4.288A pdb=" N SER A2457 " --> pdb=" O GLU A2454 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A2463 " --> pdb=" O LYS A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2500 Processing helix chain 'A' and resid 2522 through 2524 No H-bonds generated for 'chain 'A' and resid 2522 through 2524' Processing helix chain 'A' and resid 2551 through 2563 Processing helix chain 'A' and resid 2572 through 2588 Processing helix chain 'A' and resid 2601 through 2614 Processing helix chain 'A' and resid 2618 through 2629 Processing helix chain 'A' and resid 2643 through 2653 Processing helix chain 'A' and resid 2661 through 2668 Processing helix chain 'A' and resid 2674 through 2676 No H-bonds generated for 'chain 'A' and resid 2674 through 2676' Processing helix chain 'A' and resid 2679 through 2696 Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'A' and resid 2738 through 2746 Processing helix chain 'A' and resid 2776 through 2790 Processing helix chain 'A' and resid 2818 through 2824 removed outlier: 4.148A pdb=" N HIS A2822 " --> pdb=" O LYS A2819 " (cutoff:3.500A) Proline residue: A2823 - end of helix Processing helix chain 'A' and resid 2852 through 2855 No H-bonds generated for 'chain 'A' and resid 2852 through 2855' Processing helix chain 'A' and resid 2868 through 2881 removed outlier: 5.174A pdb=" N SER A2881 " --> pdb=" O GLY A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2906 removed outlier: 5.893A pdb=" N GLY A2891 " --> pdb=" O ASP A2887 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A2893 " --> pdb=" O ILE A2889 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A2894 " --> pdb=" O ARG A2890 " (cutoff:3.500A) Proline residue: A2895 - end of helix Processing helix chain 'A' and resid 2914 through 2931 Processing helix chain 'A' and resid 2937 through 2947 Processing helix chain 'A' and resid 2956 through 2962 Processing helix chain 'A' and resid 2975 through 2983 Processing helix chain 'A' and resid 3011 through 3017 Processing helix chain 'A' and resid 3038 through 3055 Processing helix chain 'A' and resid 3072 through 3076 Processing helix chain 'A' and resid 3113 through 3119 Processing helix chain 'A' and resid 3125 through 3127 No H-bonds generated for 'chain 'A' and resid 3125 through 3127' Processing helix chain 'A' and resid 3141 through 3158 Processing helix chain 'A' and resid 3173 through 3176 No H-bonds generated for 'chain 'A' and resid 3173 through 3176' Processing helix chain 'A' and resid 3184 through 3196 Processing helix chain 'A' and resid 3205 through 3220 removed outlier: 3.916A pdb=" N CYS A3220 " --> pdb=" O ILE A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.671A pdb=" N SER A3230 " --> pdb=" O VAL A3226 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLY A3231 " --> pdb=" O VAL A3227 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3248 Processing helix chain 'A' and resid 3255 through 3262 Processing helix chain 'A' and resid 3288 through 3296 Processing helix chain 'A' and resid 3308 through 3310 No H-bonds generated for 'chain 'A' and resid 3308 through 3310' Processing helix chain 'A' and resid 3314 through 3325 Processing helix chain 'A' and resid 3349 through 3364 Processing helix chain 'A' and resid 3414 through 3419 Processing helix chain 'A' and resid 3422 through 3426 removed outlier: 3.821A pdb=" N PHE A3426 " --> pdb=" O ILE A3422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3422 through 3426' Processing helix chain 'A' and resid 3477 through 3491 removed outlier: 4.979A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3511 Processing helix chain 'A' and resid 3518 through 3539 Processing helix chain 'A' and resid 3549 through 3554 Processing helix chain 'A' and resid 3557 through 3563 Processing helix chain 'A' and resid 3566 through 3589 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3596 through 3599 No H-bonds generated for 'chain 'A' and resid 3596 through 3599' Processing helix chain 'A' and resid 3605 through 3614 Processing helix chain 'A' and resid 3658 through 3675 Processing helix chain 'A' and resid 3681 through 3690 Processing helix chain 'A' and resid 3693 through 3698 Processing helix chain 'A' and resid 3703 through 3721 Processing helix chain 'A' and resid 3728 through 3745 Processing helix chain 'A' and resid 3763 through 3783 removed outlier: 7.729A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3799 removed outlier: 5.790A pdb=" N ALA A3796 " --> pdb=" O SER A3793 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A3799 " --> pdb=" O ALA A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3808 through 3823 removed outlier: 3.671A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3838 Processing helix chain 'A' and resid 3840 through 3846 Processing helix chain 'A' and resid 3857 through 3889 removed outlier: 5.300A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3909 removed outlier: 4.072A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3940 Processing helix chain 'A' and resid 3968 through 3974 Processing helix chain 'A' and resid 4000 through 4025 Processing helix chain 'A' and resid 4036 through 4045 Processing helix chain 'A' and resid 4083 through 4088 Processing helix chain 'A' and resid 4093 through 4095 No H-bonds generated for 'chain 'A' and resid 4093 through 4095' Processing helix chain 'A' and resid 4097 through 4110 Processing helix chain 'A' and resid 4117 through 4137 Processing helix chain 'A' and resid 4143 through 4155 Processing helix chain 'A' and resid 4172 through 4197 removed outlier: 3.646A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4205 through 4218 Processing helix chain 'A' and resid 4223 through 4235 Processing helix chain 'A' and resid 4238 through 4245 Processing helix chain 'A' and resid 4252 through 4254 No H-bonds generated for 'chain 'A' and resid 4252 through 4254' Processing helix chain 'A' and resid 4257 through 4261 removed outlier: 3.914A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4257 through 4261' Processing helix chain 'A' and resid 4272 through 4275 removed outlier: 3.842A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4272 through 4275' Processing helix chain 'A' and resid 4280 through 4292 Processing helix chain 'A' and resid 4297 through 4303 Processing helix chain 'A' and resid 4310 through 4330 Processing helix chain 'A' and resid 4343 through 4352 Processing helix chain 'A' and resid 4359 through 4369 removed outlier: 3.554A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) Processing helix chain 'A' and resid 4385 through 4402 Processing helix chain 'A' and resid 4406 through 4416 Proline residue: A4410 - end of helix removed outlier: 4.168A pdb=" N PHE A4416 " --> pdb=" O ASN A4413 " (cutoff:3.500A) Processing helix chain 'A' and resid 4418 through 4420 No H-bonds generated for 'chain 'A' and resid 4418 through 4420' Processing helix chain 'A' and resid 4523 through 4543 removed outlier: 3.824A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) Processing helix chain 'A' and resid 4545 through 4551 Processing helix chain 'A' and resid 4560 through 4577 Processing helix chain 'A' and resid 4582 through 4596 Processing helix chain 'A' and resid 4614 through 4634 removed outlier: 4.516A pdb=" N HIS A4634 " --> pdb=" O ARG A4630 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4648 Processing helix chain 'A' and resid 4656 through 4659 No H-bonds generated for 'chain 'A' and resid 4656 through 4659' Processing helix chain 'A' and resid 4666 through 4668 No H-bonds generated for 'chain 'A' and resid 4666 through 4668' Processing helix chain 'A' and resid 4692 through 4701 Processing helix chain 'A' and resid 4709 through 4716 Processing helix chain 'A' and resid 4718 through 4740 removed outlier: 4.758A pdb=" N LEU A4723 " --> pdb=" O ALA A4719 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A4724 " --> pdb=" O GLU A4720 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS A4725 " --> pdb=" O LEU A4721 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A4727 " --> pdb=" O LEU A4723 " (cutoff:3.500A) Proline residue: A4728 - end of helix Processing helix chain 'A' and resid 4752 through 4756 Processing helix chain 'A' and resid 4762 through 4782 Processing helix chain 'A' and resid 4786 through 4789 No H-bonds generated for 'chain 'A' and resid 4786 through 4789' Processing helix chain 'A' and resid 4821 through 4844 Processing helix chain 'A' and resid 4860 through 4862 No H-bonds generated for 'chain 'A' and resid 4860 through 4862' Processing helix chain 'A' and resid 4868 through 4871 No H-bonds generated for 'chain 'A' and resid 4868 through 4871' Processing helix chain 'A' and resid 4873 through 4877 Processing helix chain 'A' and resid 4896 through 4904 Processing helix chain 'A' and resid 4931 through 4940 Processing helix chain 'A' and resid 4948 through 4956 removed outlier: 3.837A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4961 through 4979 Processing helix chain 'A' and resid 4989 through 4993 Processing helix chain 'A' and resid 5004 through 5012 removed outlier: 5.283A pdb=" N ARG A5012 " --> pdb=" O LYS A5008 " (cutoff:3.500A) Processing helix chain 'A' and resid 5015 through 5035 removed outlier: 3.923A pdb=" N ILE A5018 " --> pdb=" O LEU A5015 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A5019 " --> pdb=" O ARG A5016 " (cutoff:3.500A) Processing helix chain 'A' and resid 5046 through 5048 No H-bonds generated for 'chain 'A' and resid 5046 through 5048' Processing helix chain 'A' and resid 5054 through 5065 Processing helix chain 'A' and resid 5069 through 5083 removed outlier: 4.283A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5099 through 5108 Processing helix chain 'A' and resid 5115 through 5120 Processing helix chain 'A' and resid 5132 through 5148 Processing sheet with id= A, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id= B, first strand: chain 'A' and resid 1625 through 1627 removed outlier: 3.673A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 7.151A pdb=" N LEU A1888 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A1795 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A1890 " --> pdb=" O ILE A1795 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 7.654A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY A1949 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR A2057 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A1951 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A2059 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER A1953 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A2061 " --> pdb=" O SER A1953 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A2014 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A2058 " --> pdb=" O VAL A2014 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A2016 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU A2060 " --> pdb=" O PHE A2016 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE A2018 " --> pdb=" O GLU A2060 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE A2020 " --> pdb=" O PRO A2062 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id= F, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id= G, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id= H, first strand: chain 'A' and resid 2377 through 2380 removed outlier: 4.388A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A2443 " --> pdb=" O HIS A2480 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A2482 " --> pdb=" O THR A2443 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A2445 " --> pdb=" O ILE A2482 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA A2484 " --> pdb=" O LEU A2445 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE A2447 " --> pdb=" O ALA A2484 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2859 through 2862 removed outlier: 6.216A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 3130 through 3132 removed outlier: 6.148A pdb=" N LEU A3003 " --> pdb=" O HIS A3131 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3080 through 3082 Processing sheet with id= L, first strand: chain 'A' and resid 3397 through 3399 removed outlier: 6.492A pdb=" N VAL A3371 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A3275 " --> pdb=" O VAL A3371 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A3373 " --> pdb=" O THR A3275 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE A3277 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A3375 " --> pdb=" O ILE A3277 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR A3279 " --> pdb=" O PHE A3375 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A3377 " --> pdb=" O THR A3279 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 4880 through 4883 1537 hydrogen bonds defined for protein. 4458 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: 22.14 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10236 1.33 - 1.46: 7316 1.46 - 1.58: 18095 1.58 - 1.70: 5 1.70 - 1.82: 303 Bond restraints: 35955 Sorted by residual: bond pdb=" C4 ATP A5201 " pdb=" C5 ATP A5201 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C5 ATP A5201 " pdb=" C6 ATP A5201 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.28e+01 bond pdb=" C5 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" C8 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.310 1.350 -0.040 1.00e-02 1.00e+04 1.61e+01 ... (remaining 35950 not shown) Histogram of bond angle deviations from ideal: 96.41 - 104.37: 542 104.37 - 112.34: 17860 112.34 - 120.31: 16897 120.31 - 128.27: 13017 128.27 - 136.24: 347 Bond angle restraints: 48663 Sorted by residual: angle pdb=" PB ATP A5201 " pdb=" O3B ATP A5201 " pdb=" PG ATP A5201 " ideal model delta sigma weight residual 139.87 121.13 18.74 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PA ATP A5201 " pdb=" O3A ATP A5201 " pdb=" PB ATP A5201 " ideal model delta sigma weight residual 136.83 121.91 14.92 1.00e+00 1.00e+00 2.23e+02 angle pdb=" C5 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N3 ATP A5201 " ideal model delta sigma weight residual 126.80 118.94 7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" N3 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.35e+01 angle pdb=" N GLU A4279 " pdb=" CA GLU A4279 " pdb=" C GLU A4279 " ideal model delta sigma weight residual 114.56 107.03 7.53 1.27e+00 6.20e-01 3.52e+01 ... (remaining 48658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 20577 16.70 - 33.40: 1088 33.40 - 50.10: 197 50.10 - 66.79: 16 66.79 - 83.49: 34 Dihedral angle restraints: 21912 sinusoidal: 8926 harmonic: 12986 Sorted by residual: dihedral pdb=" CA VAL A3122 " pdb=" C VAL A3122 " pdb=" N PRO A3123 " pdb=" CA PRO A3123 " ideal model delta harmonic sigma weight residual 180.00 119.33 60.67 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 132.87 47.13 0 5.00e+00 4.00e-02 8.88e+01 dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -136.64 -43.36 0 5.00e+00 4.00e-02 7.52e+01 ... (remaining 21909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4550 0.080 - 0.159: 860 0.159 - 0.239: 88 0.239 - 0.318: 7 0.318 - 0.398: 6 Chirality restraints: 5511 Sorted by residual: chirality pdb=" CB ILE A1373 " pdb=" CA ILE A1373 " pdb=" CG1 ILE A1373 " pdb=" CG2 ILE A1373 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE A 896 " pdb=" CA ILE A 896 " pdb=" CG1 ILE A 896 " pdb=" CG2 ILE A 896 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL A4048 " pdb=" CA VAL A4048 " pdb=" CG1 VAL A4048 " pdb=" CG2 VAL A4048 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5508 not shown) Planarity restraints: 6228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A3123 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 687 " -0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 688 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A5023 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLN A5023 " 0.063 2.00e-02 2.50e+03 pdb=" O GLN A5023 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A5024 " -0.021 2.00e-02 2.50e+03 ... (remaining 6225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 393 2.63 - 3.20: 31500 3.20 - 3.77: 55974 3.77 - 4.33: 76296 4.33 - 4.90: 123574 Nonbonded interactions: 287737 Sorted by model distance: nonbonded pdb=" OG SER A1961 " pdb="MG MG A5202 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR A1820 " pdb=" OD1 ASP A1822 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A1666 " pdb=" O MET A1690 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A3664 " pdb=" OG1 THR A3692 " model vdw 2.273 2.440 nonbonded pdb=" O LEU A2945 " pdb=" OG SER A2949 " model vdw 2.274 2.440 ... (remaining 287732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.860 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 104.750 Find NCS groups from input model: 1.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.009 0.108 35955 Z= 0.595 Angle : 1.127 19.136 48663 Z= 0.606 Chirality : 0.063 0.398 5511 Planarity : 0.008 0.114 6228 Dihedral : 11.276 83.492 13448 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.49 % Favored : 90.32 % Rotamer: Outliers : 0.46 % Allowed : 2.82 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.81 % Twisted General : 0.14 % 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: -4.10 (0.10), residues: 4319 helix: -2.34 (0.08), residues: 2479 sheet: -1.45 (0.31), residues: 232 loop : -3.35 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A5135 HIS 0.023 0.003 HIS A2688 PHE 0.058 0.004 PHE A2960 TYR 0.048 0.004 TYR A2057 ARG 0.018 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 473 time to evaluate : 4.009 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7354 (mm110) REVERT: A 874 LEU cc_start: 0.8139 (tt) cc_final: 0.7900 (mt) REVERT: A 1256 LEU cc_start: 0.8957 (mt) cc_final: 0.8580 (mt) REVERT: A 1275 ASP cc_start: 0.7833 (t0) cc_final: 0.7610 (t0) REVERT: A 1378 GLN cc_start: 0.7237 (tt0) cc_final: 0.6789 (tt0) REVERT: A 1521 SER cc_start: 0.8542 (m) cc_final: 0.8305 (p) REVERT: A 2164 ILE cc_start: 0.8434 (tt) cc_final: 0.8167 (pt) REVERT: A 2215 PHE cc_start: 0.7836 (t80) cc_final: 0.7585 (t80) REVERT: A 2216 MET cc_start: 0.7092 (mmt) cc_final: 0.6593 (mmt) REVERT: A 2304 LYS cc_start: 0.8395 (mttp) cc_final: 0.8162 (mmmm) REVERT: A 2420 MET cc_start: 0.8342 (mtt) cc_final: 0.8117 (mtt) REVERT: A 2476 ASP cc_start: 0.6899 (p0) cc_final: 0.6682 (p0) REVERT: A 2801 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8888 (m) REVERT: A 2923 MET cc_start: 0.8420 (mtp) cc_final: 0.8098 (mtt) REVERT: A 3644 HIS cc_start: 0.7174 (m170) cc_final: 0.6126 (m-70) REVERT: A 3675 ILE cc_start: 0.8101 (mt) cc_final: 0.7729 (tt) REVERT: A 3984 TYR cc_start: 0.8607 (t80) cc_final: 0.8405 (t80) REVERT: A 4003 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8527 (tppt) REVERT: A 4007 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8242 (pttt) REVERT: A 4316 TYR cc_start: 0.7157 (m-10) cc_final: 0.6780 (m-10) REVERT: A 4356 LEU cc_start: 0.8718 (pt) cc_final: 0.8476 (pp) REVERT: A 4507 SER cc_start: 0.8272 (m) cc_final: 0.8071 (t) REVERT: A 4600 GLN cc_start: 0.7003 (mp-120) cc_final: 0.6749 (mp10) REVERT: A 4668 PHE cc_start: 0.7427 (p90) cc_final: 0.7119 (p90) REVERT: A 4856 SER cc_start: 0.7697 (m) cc_final: 0.7451 (p) REVERT: A 4941 MET cc_start: 0.7240 (mtp) cc_final: 0.6997 (mtp) REVERT: A 5084 LEU cc_start: 0.8590 (mt) cc_final: 0.8359 (mp) REVERT: A 5107 MET cc_start: 0.6979 (tmm) cc_final: 0.6284 (tmm) REVERT: A 5127 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8229 (tm) REVERT: A 5146 GLN cc_start: 0.7617 (pt0) cc_final: 0.7289 (tm-30) outliers start: 18 outliers final: 5 residues processed: 489 average time/residue: 0.6504 time to fit residues: 483.2373 Evaluate side-chains 307 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 300 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 2801 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN A 822 HIS A 827 ASN A 831 ASN A1089 HIS A1186 HIS A1378 GLN A1429 HIS A1453 ASN A1579 ASN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 HIS A1770 HIS A1791 GLN A1816 GLN A1920 ASN A1930 GLN A2139 GLN A2161 HIS A2273 HIS A2480 HIS ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2677 ASN A2790 GLN A2942 HIS A2981 GLN A3013 GLN ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 HIS A3252 HIS A3337 GLN A3542 GLN A3575 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3644 HIS A3705 GLN A3914 ASN A4008 HIS A4176 GLN A4196 GLN A4242 GLN A4249 HIS ** A4252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4382 ASN A4420 ASN A4543 HIS A4560 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4587 HIS A4674 GLN A4697 HIS A4757 HIS A4834 HIS ** A4842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN A4879 ASN A4886 GLN A4892 GLN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4932 HIS A4957 GLN A5017 HIS A5028 HIS A5056 HIS A5146 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35955 Z= 0.202 Angle : 0.652 12.376 48663 Z= 0.333 Chirality : 0.042 0.266 5511 Planarity : 0.005 0.091 6228 Dihedral : 6.471 87.760 4806 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.60 % Rotamer: Outliers : 1.21 % Allowed : 7.03 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.02 % 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: -2.26 (0.12), residues: 4319 helix: -0.58 (0.10), residues: 2456 sheet: -1.15 (0.32), residues: 240 loop : -2.97 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A3659 HIS 0.009 0.001 HIS A4587 PHE 0.035 0.002 PHE A2371 TYR 0.027 0.002 TYR A3901 ARG 0.008 0.001 ARG A4155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 3.951 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7418 (mm110) REVERT: A 1166 LYS cc_start: 0.8404 (mttt) cc_final: 0.8135 (ttmt) REVERT: A 1327 ARG cc_start: 0.7861 (tmm160) cc_final: 0.7652 (ttp80) REVERT: A 1905 PHE cc_start: 0.7831 (m-10) cc_final: 0.7606 (m-80) REVERT: A 2164 ILE cc_start: 0.8544 (tt) cc_final: 0.8260 (pt) REVERT: A 2215 PHE cc_start: 0.7580 (t80) cc_final: 0.7341 (t80) REVERT: A 2304 LYS cc_start: 0.8286 (mttp) cc_final: 0.8051 (mtpp) REVERT: A 2407 MET cc_start: 0.8219 (ttt) cc_final: 0.7946 (ttt) REVERT: A 2801 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8835 (m) REVERT: A 2923 MET cc_start: 0.8412 (mtp) cc_final: 0.8152 (mtt) REVERT: A 3684 LYS cc_start: 0.8273 (tppt) cc_final: 0.8058 (tppt) REVERT: A 3814 MET cc_start: 0.7973 (ttm) cc_final: 0.7530 (tpp) REVERT: A 3984 TYR cc_start: 0.8478 (t80) cc_final: 0.7884 (t80) REVERT: A 4003 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8095 (tppt) REVERT: A 4007 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8263 (pttt) REVERT: A 4255 PHE cc_start: 0.7501 (m-10) cc_final: 0.7213 (m-10) REVERT: A 4289 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8216 (ttpt) REVERT: A 4507 SER cc_start: 0.8268 (m) cc_final: 0.7988 (p) REVERT: A 4668 PHE cc_start: 0.7437 (p90) cc_final: 0.7128 (p90) REVERT: A 4856 SER cc_start: 0.7624 (m) cc_final: 0.7238 (p) REVERT: A 4908 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8190 (pt) REVERT: A 4941 MET cc_start: 0.7234 (mtp) cc_final: 0.7002 (mtp) REVERT: A 5084 LEU cc_start: 0.8444 (mt) cc_final: 0.8209 (mp) REVERT: A 5127 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8048 (tm) REVERT: A 5146 GLN cc_start: 0.7553 (pt0) cc_final: 0.7283 (tm-30) outliers start: 47 outliers final: 24 residues processed: 349 average time/residue: 0.5318 time to fit residues: 292.6848 Evaluate side-chains 307 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 280 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2801 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2908 ASP Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4674 GLN Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 334 optimal weight: 0.9980 chunk 273 optimal weight: 0.0070 chunk 110 optimal weight: 1.9990 chunk 402 optimal weight: 5.9990 chunk 434 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 322 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A1378 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1757 HIS A2273 HIS ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3037 GLN A3600 GLN ** A3871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4176 GLN ** A4252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4623 HIS A4674 GLN A4713 HIS A4757 HIS ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35955 Z= 0.187 Angle : 0.611 11.352 48663 Z= 0.309 Chirality : 0.041 0.188 5511 Planarity : 0.005 0.094 6228 Dihedral : 6.047 87.713 4806 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.59 % Favored : 91.36 % Rotamer: Outliers : 1.62 % Allowed : 8.10 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.02 % 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: -1.45 (0.13), residues: 4319 helix: 0.16 (0.10), residues: 2464 sheet: -1.07 (0.32), residues: 241 loop : -2.75 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4555 HIS 0.008 0.001 HIS A3644 PHE 0.031 0.001 PHE A2371 TYR 0.022 0.001 TYR A2146 ARG 0.008 0.000 ARG A4630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 3.810 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7429 (mm110) REVERT: A 1166 LYS cc_start: 0.8410 (mttt) cc_final: 0.8198 (ttmt) REVERT: A 1275 ASP cc_start: 0.7604 (t0) cc_final: 0.7341 (t0) REVERT: A 1327 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7670 (tmm160) REVERT: A 1596 MET cc_start: 0.7568 (mmm) cc_final: 0.7014 (mmm) REVERT: A 1905 PHE cc_start: 0.7788 (m-10) cc_final: 0.7537 (m-80) REVERT: A 2164 ILE cc_start: 0.8574 (tt) cc_final: 0.8346 (pt) REVERT: A 2215 PHE cc_start: 0.7648 (t80) cc_final: 0.7363 (t80) REVERT: A 2216 MET cc_start: 0.7214 (mmm) cc_final: 0.6997 (mmt) REVERT: A 2304 LYS cc_start: 0.8278 (mttp) cc_final: 0.8065 (mtpp) REVERT: A 2380 MET cc_start: 0.7630 (ttm) cc_final: 0.7285 (ttm) REVERT: A 2923 MET cc_start: 0.8402 (mtp) cc_final: 0.8147 (mtt) REVERT: A 3691 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7411 (mmtm) REVERT: A 3814 MET cc_start: 0.8003 (ttm) cc_final: 0.7560 (tpp) REVERT: A 4002 ARG cc_start: 0.7595 (tpp-160) cc_final: 0.7359 (tpp-160) REVERT: A 4007 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8217 (mttm) REVERT: A 4014 MET cc_start: 0.7224 (mtm) cc_final: 0.6932 (mtm) REVERT: A 4255 PHE cc_start: 0.7643 (m-10) cc_final: 0.7280 (m-10) REVERT: A 4289 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8244 (ttpt) REVERT: A 4507 SER cc_start: 0.8231 (m) cc_final: 0.7971 (p) REVERT: A 4668 PHE cc_start: 0.7431 (p90) cc_final: 0.7143 (p90) REVERT: A 4739 LYS cc_start: 0.7840 (tmtt) cc_final: 0.7605 (tttm) REVERT: A 4908 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8214 (pt) REVERT: A 5084 LEU cc_start: 0.8449 (mt) cc_final: 0.8189 (mp) REVERT: A 5127 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7993 (tm) REVERT: A 5146 GLN cc_start: 0.7572 (pt0) cc_final: 0.7296 (tm-30) outliers start: 63 outliers final: 28 residues processed: 346 average time/residue: 0.6029 time to fit residues: 329.3953 Evaluate side-chains 299 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 269 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1339 ASN Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2908 ASP Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 191 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 403 optimal weight: 0.8980 chunk 427 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 382 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A1378 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3017 GLN A3705 GLN ** A3871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4713 HIS A4757 HIS A5014 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35955 Z= 0.182 Angle : 0.597 10.694 48663 Z= 0.299 Chirality : 0.041 0.206 5511 Planarity : 0.004 0.093 6228 Dihedral : 5.815 87.672 4805 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.54 % Favored : 91.41 % Rotamer: Outliers : 1.90 % Allowed : 8.67 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4319 helix: 0.54 (0.11), residues: 2456 sheet: -0.91 (0.32), residues: 249 loop : -2.62 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4555 HIS 0.005 0.001 HIS A3644 PHE 0.027 0.001 PHE A2371 TYR 0.021 0.001 TYR A2146 ARG 0.006 0.000 ARG A3662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 282 time to evaluate : 3.940 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7451 (mm110) REVERT: A 1275 ASP cc_start: 0.7590 (t0) cc_final: 0.7114 (t0) REVERT: A 1327 ARG cc_start: 0.7931 (tmm160) cc_final: 0.7714 (tmm160) REVERT: A 1905 PHE cc_start: 0.7812 (m-10) cc_final: 0.7556 (m-80) REVERT: A 2024 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7358 (t) REVERT: A 2215 PHE cc_start: 0.7661 (t80) cc_final: 0.7407 (t80) REVERT: A 2216 MET cc_start: 0.7162 (mmm) cc_final: 0.6961 (mmp) REVERT: A 2304 LYS cc_start: 0.8384 (mttp) cc_final: 0.8159 (mtpp) REVERT: A 2380 MET cc_start: 0.7649 (ttm) cc_final: 0.7241 (ttm) REVERT: A 2855 MET cc_start: 0.6362 (mpp) cc_final: 0.5438 (mpp) REVERT: A 2923 MET cc_start: 0.8404 (mtp) cc_final: 0.8147 (mtt) REVERT: A 3691 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7403 (mmtm) REVERT: A 4206 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7398 (mpt90) REVERT: A 4244 PHE cc_start: 0.7925 (m-80) cc_final: 0.7590 (t80) REVERT: A 4255 PHE cc_start: 0.7690 (m-10) cc_final: 0.7318 (m-10) REVERT: A 4289 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8286 (ttpt) REVERT: A 4507 SER cc_start: 0.8201 (m) cc_final: 0.7957 (p) REVERT: A 4668 PHE cc_start: 0.7409 (p90) cc_final: 0.7154 (p90) REVERT: A 4739 LYS cc_start: 0.7852 (tmtt) cc_final: 0.7628 (tttm) REVERT: A 4908 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8205 (pt) REVERT: A 5084 LEU cc_start: 0.8442 (mt) cc_final: 0.8100 (mt) REVERT: A 5107 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6804 (tpp) REVERT: A 5127 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (tm) REVERT: A 5128 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7413 (tpt) REVERT: A 5146 GLN cc_start: 0.7577 (pt0) cc_final: 0.7336 (tm-30) outliers start: 74 outliers final: 41 residues processed: 329 average time/residue: 0.5451 time to fit residues: 284.4662 Evaluate side-chains 313 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 267 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1339 ASN Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2908 ASP Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3652 TYR Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5107 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 9.9990 chunk 242 optimal weight: 0.0030 chunk 6 optimal weight: 0.0270 chunk 318 optimal weight: 0.0370 chunk 176 optimal weight: 3.9990 chunk 364 optimal weight: 6.9990 chunk 295 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A1595 ASN A2139 GLN ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3538 GLN ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3799 HIS ** A3871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4276 HIS ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4679 HIS A4757 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35955 Z= 0.137 Angle : 0.572 10.104 48663 Z= 0.287 Chirality : 0.040 0.193 5511 Planarity : 0.004 0.090 6228 Dihedral : 5.593 88.079 4805 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.10 % Favored : 91.87 % Rotamer: Outliers : 1.64 % Allowed : 9.44 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.69 (0.13), residues: 4319 helix: 0.83 (0.11), residues: 2456 sheet: -0.81 (0.33), residues: 242 loop : -2.50 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2541 HIS 0.004 0.001 HIS A1454 PHE 0.021 0.001 PHE A2371 TYR 0.018 0.001 TYR A2146 ARG 0.006 0.000 ARG A2319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 4.187 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 795 MET cc_start: 0.7361 (mtm) cc_final: 0.7158 (mtm) REVERT: A 1275 ASP cc_start: 0.7537 (t0) cc_final: 0.7039 (t0) REVERT: A 1327 ARG cc_start: 0.7940 (tmm160) cc_final: 0.7713 (tmm160) REVERT: A 1596 MET cc_start: 0.7394 (mmm) cc_final: 0.6993 (mmp) REVERT: A 1905 PHE cc_start: 0.7753 (m-80) cc_final: 0.7515 (m-80) REVERT: A 2205 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6925 (tt) REVERT: A 2215 PHE cc_start: 0.7609 (t80) cc_final: 0.7351 (t80) REVERT: A 2307 MET cc_start: 0.7348 (ttp) cc_final: 0.6799 (ttm) REVERT: A 2855 MET cc_start: 0.6375 (mpp) cc_final: 0.5539 (mpp) REVERT: A 2923 MET cc_start: 0.8362 (mtp) cc_final: 0.8085 (mtt) REVERT: A 3691 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7367 (mmtm) REVERT: A 4255 PHE cc_start: 0.7625 (m-10) cc_final: 0.7306 (m-10) REVERT: A 4289 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8282 (ttmt) REVERT: A 4297 LEU cc_start: 0.8017 (tp) cc_final: 0.7765 (tp) REVERT: A 4507 SER cc_start: 0.8156 (m) cc_final: 0.7928 (p) REVERT: A 4739 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7583 (tttm) REVERT: A 4908 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8223 (pt) REVERT: A 5127 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7849 (tm) outliers start: 64 outliers final: 35 residues processed: 323 average time/residue: 0.5333 time to fit residues: 276.6780 Evaluate side-chains 295 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3652 TYR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4634 HIS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 5127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.0040 chunk 384 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 250 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 427 optimal weight: 0.9990 chunk 355 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A 749 ASN A2145 GLN ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3600 GLN ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3871 ASN A4560 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4713 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35955 Z= 0.156 Angle : 0.580 12.467 48663 Z= 0.289 Chirality : 0.040 0.259 5511 Planarity : 0.004 0.088 6228 Dihedral : 5.492 88.351 4804 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.08 % Favored : 91.90 % Rotamer: Outliers : 1.87 % Allowed : 9.92 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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 (0.13), residues: 4319 helix: 0.96 (0.11), residues: 2454 sheet: -0.68 (0.33), residues: 242 loop : -2.37 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4555 HIS 0.005 0.001 HIS A 796 PHE 0.031 0.001 PHE A2312 TYR 0.027 0.001 TYR A4316 ARG 0.007 0.000 ARG A2319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 268 time to evaluate : 3.830 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7853 (mp) REVERT: A 671 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6089 (pt) REVERT: A 795 MET cc_start: 0.7431 (mtm) cc_final: 0.7203 (mtm) REVERT: A 1275 ASP cc_start: 0.7554 (t0) cc_final: 0.7049 (t0) REVERT: A 1327 ARG cc_start: 0.7972 (tmm160) cc_final: 0.7726 (tmm160) REVERT: A 1596 MET cc_start: 0.7403 (mmm) cc_final: 0.6962 (mmp) REVERT: A 1823 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.3992 (mp0) REVERT: A 1905 PHE cc_start: 0.7779 (m-80) cc_final: 0.7539 (m-80) REVERT: A 2205 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6992 (tt) REVERT: A 2215 PHE cc_start: 0.7606 (t80) cc_final: 0.7365 (t80) REVERT: A 2319 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7973 (mtm-85) REVERT: A 2855 MET cc_start: 0.6435 (mpp) cc_final: 0.5658 (mpp) REVERT: A 2923 MET cc_start: 0.8383 (mtp) cc_final: 0.8139 (mtm) REVERT: A 3691 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7252 (mmtm) REVERT: A 3921 PHE cc_start: 0.6688 (t80) cc_final: 0.6402 (t80) REVERT: A 4002 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7173 (tpp-160) REVERT: A 4003 LYS cc_start: 0.8643 (tppt) cc_final: 0.8393 (tptp) REVERT: A 4244 PHE cc_start: 0.7874 (m-80) cc_final: 0.7596 (t80) REVERT: A 4255 PHE cc_start: 0.7633 (m-10) cc_final: 0.7294 (m-10) REVERT: A 4289 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8292 (ttpt) REVERT: A 4297 LEU cc_start: 0.8012 (tp) cc_final: 0.7750 (tp) REVERT: A 4373 LEU cc_start: 0.6645 (mt) cc_final: 0.6421 (mt) REVERT: A 4507 SER cc_start: 0.8138 (m) cc_final: 0.7918 (p) REVERT: A 4739 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7620 (tttm) REVERT: A 4753 ARG cc_start: 0.7049 (ttp80) cc_final: 0.6807 (tpt90) REVERT: A 4908 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8225 (pt) REVERT: A 5107 MET cc_start: 0.7239 (tpp) cc_final: 0.6901 (tpp) REVERT: A 5127 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7683 (tp) REVERT: A 5128 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7313 (tpt) outliers start: 73 outliers final: 47 residues processed: 324 average time/residue: 0.5112 time to fit residues: 268.0135 Evaluate side-chains 312 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 258 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1339 ASN Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2908 ASP Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3652 TYR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3958 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4378 ILE Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.4980 chunk 48 optimal weight: 0.0060 chunk 243 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 359 optimal weight: 0.0670 chunk 238 optimal weight: 4.9990 chunk 426 optimal weight: 0.0060 chunk 266 optimal weight: 0.0870 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.1328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A1378 GLN A1395 HIS A2560 GLN A3392 HIS A3644 HIS ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35955 Z= 0.130 Angle : 0.570 11.689 48663 Z= 0.282 Chirality : 0.039 0.239 5511 Planarity : 0.004 0.089 6228 Dihedral : 5.303 85.846 4804 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.57 % Favored : 92.41 % Rotamer: Outliers : 1.51 % Allowed : 10.49 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.30 (0.13), residues: 4319 helix: 1.16 (0.11), residues: 2446 sheet: -0.54 (0.33), residues: 235 loop : -2.35 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4555 HIS 0.006 0.001 HIS A1454 PHE 0.023 0.001 PHE A2082 TYR 0.028 0.001 TYR A4316 ARG 0.009 0.000 ARG A4598 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 4.005 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 795 MET cc_start: 0.7443 (mtm) cc_final: 0.7209 (mtm) REVERT: A 1275 ASP cc_start: 0.7466 (t0) cc_final: 0.6966 (t0) REVERT: A 1327 ARG cc_start: 0.7913 (tmm160) cc_final: 0.7647 (tmm160) REVERT: A 1823 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.4085 (mp0) REVERT: A 1905 PHE cc_start: 0.7703 (m-80) cc_final: 0.7481 (m-10) REVERT: A 2205 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6835 (tt) REVERT: A 2215 PHE cc_start: 0.7598 (t80) cc_final: 0.7357 (t80) REVERT: A 2855 MET cc_start: 0.6296 (mpp) cc_final: 0.5544 (mpp) REVERT: A 3691 LYS cc_start: 0.7551 (mmtm) cc_final: 0.7249 (mmtm) REVERT: A 3814 MET cc_start: 0.7874 (ttm) cc_final: 0.7666 (tpp) REVERT: A 3921 PHE cc_start: 0.6689 (t80) cc_final: 0.6393 (t80) REVERT: A 4002 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7079 (tpp-160) REVERT: A 4003 LYS cc_start: 0.8597 (tppt) cc_final: 0.8387 (tptp) REVERT: A 4244 PHE cc_start: 0.7751 (m-80) cc_final: 0.7525 (t80) REVERT: A 4255 PHE cc_start: 0.7486 (m-10) cc_final: 0.7154 (m-10) REVERT: A 4289 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8299 (ttpt) REVERT: A 4373 LEU cc_start: 0.6504 (mt) cc_final: 0.6273 (mt) REVERT: A 4507 SER cc_start: 0.8076 (m) cc_final: 0.7858 (p) REVERT: A 4713 HIS cc_start: 0.7376 (t70) cc_final: 0.6894 (t70) REVERT: A 4717 LYS cc_start: 0.7982 (pttt) cc_final: 0.7608 (pttt) REVERT: A 4739 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7507 (tttm) REVERT: A 4908 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8238 (pt) REVERT: A 5127 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 5128 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7190 (tpt) outliers start: 59 outliers final: 38 residues processed: 324 average time/residue: 0.5383 time to fit residues: 277.7956 Evaluate side-chains 297 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 253 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3652 TYR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3958 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4744 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 290 optimal weight: 0.2980 chunk 210 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 334 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 683 ASN A 827 ASN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4249 HIS ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4713 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35955 Z= 0.165 Angle : 0.580 11.681 48663 Z= 0.288 Chirality : 0.040 0.322 5511 Planarity : 0.004 0.083 6228 Dihedral : 5.248 83.315 4803 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.31 % Rotamer: Outliers : 1.72 % Allowed : 10.79 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.18 (0.13), residues: 4319 helix: 1.24 (0.11), residues: 2450 sheet: -0.50 (0.34), residues: 237 loop : -2.26 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4555 HIS 0.005 0.001 HIS A 796 PHE 0.027 0.001 PHE A2371 TYR 0.025 0.001 TYR A4316 ARG 0.009 0.000 ARG A1101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 265 time to evaluate : 3.824 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 795 MET cc_start: 0.7447 (mtm) cc_final: 0.7219 (mtm) REVERT: A 1275 ASP cc_start: 0.7521 (t0) cc_final: 0.7030 (t0) REVERT: A 1596 MET cc_start: 0.7418 (mmp) cc_final: 0.7154 (mmp) REVERT: A 1823 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.3982 (mp0) REVERT: A 1905 PHE cc_start: 0.7751 (m-80) cc_final: 0.7499 (m-10) REVERT: A 2205 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6814 (tt) REVERT: A 2215 PHE cc_start: 0.7725 (t80) cc_final: 0.7429 (t80) REVERT: A 2319 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.8007 (mtm-85) REVERT: A 2855 MET cc_start: 0.6399 (mpp) cc_final: 0.5600 (mpp) REVERT: A 3691 LYS cc_start: 0.7514 (mmtm) cc_final: 0.7179 (mmtm) REVERT: A 3814 MET cc_start: 0.7895 (ttm) cc_final: 0.7671 (tpp) REVERT: A 3921 PHE cc_start: 0.6770 (t80) cc_final: 0.6502 (t80) REVERT: A 3981 MET cc_start: 0.7286 (tmm) cc_final: 0.7059 (tmm) REVERT: A 4002 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7159 (tpp-160) REVERT: A 4003 LYS cc_start: 0.8626 (tppt) cc_final: 0.8389 (tptp) REVERT: A 4244 PHE cc_start: 0.7812 (m-80) cc_final: 0.7541 (t80) REVERT: A 4255 PHE cc_start: 0.7503 (m-10) cc_final: 0.7182 (m-10) REVERT: A 4289 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8318 (ttpt) REVERT: A 4717 LYS cc_start: 0.8035 (pttt) cc_final: 0.7808 (pttt) REVERT: A 4739 LYS cc_start: 0.7827 (tmtt) cc_final: 0.7597 (tttm) REVERT: A 4753 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6819 (tpt90) REVERT: A 4908 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8260 (pt) REVERT: A 5127 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7482 (tp) REVERT: A 5128 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7305 (tpt) outliers start: 67 outliers final: 47 residues processed: 313 average time/residue: 0.5486 time to fit residues: 272.7940 Evaluate side-chains 306 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 253 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1339 ASN Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2908 ASP Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3958 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4576 LYS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 5.9990 chunk 408 optimal weight: 4.9990 chunk 372 optimal weight: 2.9990 chunk 396 optimal weight: 6.9990 chunk 238 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 358 optimal weight: 7.9990 chunk 375 optimal weight: 0.0370 chunk 395 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A3502 ASN ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35955 Z= 0.164 Angle : 0.590 10.998 48663 Z= 0.291 Chirality : 0.040 0.331 5511 Planarity : 0.004 0.084 6228 Dihedral : 5.220 81.869 4803 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 1.64 % Allowed : 11.21 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.14 (0.13), residues: 4319 helix: 1.30 (0.11), residues: 2443 sheet: -0.45 (0.34), residues: 232 loop : -2.28 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4555 HIS 0.003 0.001 HIS A2282 PHE 0.029 0.001 PHE A2082 TYR 0.018 0.001 TYR A2146 ARG 0.020 0.000 ARG A2316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 259 time to evaluate : 4.145 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: symmetry clash REVERT: A 665 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 795 MET cc_start: 0.7429 (mtm) cc_final: 0.7218 (mtm) REVERT: A 1275 ASP cc_start: 0.7540 (t0) cc_final: 0.7048 (t0) REVERT: A 1327 ARG cc_start: 0.7965 (tmm160) cc_final: 0.7684 (ttp80) REVERT: A 1596 MET cc_start: 0.7381 (mmp) cc_final: 0.7129 (mmp) REVERT: A 1823 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.4011 (mp0) REVERT: A 1905 PHE cc_start: 0.7765 (m-80) cc_final: 0.7519 (m-10) REVERT: A 2205 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6810 (tt) REVERT: A 2215 PHE cc_start: 0.7688 (t80) cc_final: 0.7381 (t80) REVERT: A 2216 MET cc_start: 0.7182 (mmt) cc_final: 0.6908 (mmt) REVERT: A 2855 MET cc_start: 0.6373 (mpp) cc_final: 0.5584 (mpp) REVERT: A 3814 MET cc_start: 0.7909 (ttm) cc_final: 0.7570 (tpp) REVERT: A 3921 PHE cc_start: 0.6746 (t80) cc_final: 0.6494 (t80) REVERT: A 4003 LYS cc_start: 0.8634 (tppt) cc_final: 0.8387 (tptp) REVERT: A 4244 PHE cc_start: 0.7791 (m-80) cc_final: 0.7524 (t80) REVERT: A 4255 PHE cc_start: 0.7494 (m-10) cc_final: 0.7168 (m-10) REVERT: A 4289 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8316 (ttpt) REVERT: A 4717 LYS cc_start: 0.7948 (pttt) cc_final: 0.7724 (pttm) REVERT: A 4739 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7598 (tttm) REVERT: A 4870 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7454 (ttp-110) REVERT: A 4908 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (pt) REVERT: A 5127 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7463 (tp) REVERT: A 5128 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7343 (tpt) outliers start: 64 outliers final: 48 residues processed: 310 average time/residue: 0.5420 time to fit residues: 268.8562 Evaluate side-chains 307 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 253 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2276 MET Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2799 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3644 HIS Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3958 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4544 ASN Chi-restraints excluded: chain A residue 4576 LYS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.9990 chunk 419 optimal weight: 0.0020 chunk 256 optimal weight: 0.4980 chunk 199 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 chunk 405 optimal weight: 0.0060 chunk 350 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A 749 ASN A2273 HIS ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35955 Z= 0.151 Angle : 0.590 12.041 48663 Z= 0.290 Chirality : 0.040 0.326 5511 Planarity : 0.004 0.082 6228 Dihedral : 5.161 80.252 4803 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.83 % Favored : 92.15 % Rotamer: Outliers : 1.62 % Allowed : 11.26 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.08 (0.13), residues: 4319 helix: 1.35 (0.11), residues: 2442 sheet: -0.39 (0.34), residues: 232 loop : -2.26 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1459 HIS 0.003 0.001 HIS A4587 PHE 0.028 0.001 PHE A2371 TYR 0.018 0.001 TYR A1750 ARG 0.013 0.000 ARG A4002 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 256 time to evaluate : 3.965 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 665 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 1275 ASP cc_start: 0.7531 (t0) cc_final: 0.7036 (t0) REVERT: A 1327 ARG cc_start: 0.7935 (tmm160) cc_final: 0.7714 (ttp80) REVERT: A 1442 MET cc_start: 0.6587 (mmp) cc_final: 0.6161 (mmp) REVERT: A 1823 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.4008 (mp0) REVERT: A 1905 PHE cc_start: 0.7712 (m-80) cc_final: 0.7491 (m-10) REVERT: A 2205 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6809 (tt) REVERT: A 2215 PHE cc_start: 0.7670 (t80) cc_final: 0.7361 (t80) REVERT: A 2216 MET cc_start: 0.7164 (mmt) cc_final: 0.6862 (mmt) REVERT: A 2855 MET cc_start: 0.6351 (mpp) cc_final: 0.5565 (mpp) REVERT: A 3806 MET cc_start: 0.8081 (tpt) cc_final: 0.7223 (tpt) REVERT: A 3814 MET cc_start: 0.7888 (ttm) cc_final: 0.7645 (tpp) REVERT: A 3921 PHE cc_start: 0.6717 (t80) cc_final: 0.6506 (t80) REVERT: A 4003 LYS cc_start: 0.8695 (tppt) cc_final: 0.8464 (tptp) REVERT: A 4244 PHE cc_start: 0.7770 (m-80) cc_final: 0.7522 (t80) REVERT: A 4255 PHE cc_start: 0.7487 (m-10) cc_final: 0.7161 (m-10) REVERT: A 4289 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8301 (ttpt) REVERT: A 4717 LYS cc_start: 0.7936 (pttt) cc_final: 0.7724 (pttm) REVERT: A 4739 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7617 (tttm) REVERT: A 4870 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7438 (ttp-110) REVERT: A 4908 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8271 (pt) REVERT: A 5107 MET cc_start: 0.7517 (mmm) cc_final: 0.7049 (tpt) REVERT: A 5127 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7445 (tp) REVERT: A 5128 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7291 (tpt) outliers start: 63 outliers final: 49 residues processed: 305 average time/residue: 0.5512 time to fit residues: 269.8110 Evaluate side-chains 306 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1823 GLU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1948 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2205 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2557 GLN Chi-restraints excluded: chain A residue 2563 VAL Chi-restraints excluded: chain A residue 2799 VAL Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2957 LEU Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3133 LEU Chi-restraints excluded: chain A residue 3243 SER Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3519 ARG Chi-restraints excluded: chain A residue 3598 LEU Chi-restraints excluded: chain A residue 3644 HIS Chi-restraints excluded: chain A residue 3692 THR Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3757 PHE Chi-restraints excluded: chain A residue 3759 LEU Chi-restraints excluded: chain A residue 3781 ILE Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4001 HIS Chi-restraints excluded: chain A residue 4083 VAL Chi-restraints excluded: chain A residue 4544 ASN Chi-restraints excluded: chain A residue 4576 LYS Chi-restraints excluded: chain A residue 4658 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4903 ILE Chi-restraints excluded: chain A residue 4908 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 4999 MET Chi-restraints excluded: chain A residue 5127 LEU Chi-restraints excluded: chain A residue 5128 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 351 optimal weight: 0.9980 chunk 146 optimal weight: 0.0470 chunk 360 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A2273 HIS A3644 HIS ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.086332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071472 restraints weight = 114894.913| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.89 r_work: 0.3265 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35955 Z= 0.162 Angle : 0.592 11.377 48663 Z= 0.291 Chirality : 0.040 0.322 5511 Planarity : 0.004 0.083 6228 Dihedral : 5.132 79.092 4803 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 1.38 % Allowed : 11.51 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.04 (0.13), residues: 4319 helix: 1.36 (0.11), residues: 2451 sheet: -0.39 (0.34), residues: 242 loop : -2.22 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1459 HIS 0.003 0.001 HIS A4587 PHE 0.025 0.001 PHE A2371 TYR 0.018 0.001 TYR A2146 ARG 0.012 0.000 ARG A4598 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7785.14 seconds wall clock time: 143 minutes 7.06 seconds (8587.06 seconds total)