Starting phenix.real_space_refine on Thu Sep 18 16:04:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9di3_46897/09_2025/9di3_46897.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 78 5.16 5 C 11343 2.51 5 N 2965 2.21 5 O 3299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17694 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2282, 17582 Classifications: {'peptide': 2282} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 60, 'TRANS': 2221} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 910 Unresolved non-hydrogen angles: 1131 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 47, 'ASP:plan': 22, 'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 21, 'PHE:plan': 10, 'ARG:plan': 13, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 537 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.16, per 1000 atoms: 0.24 Number of scatterers: 17694 At special positions: 0 Unit cell: (111.36, 156.6, 155.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 9 15.00 O 3299 8.00 N 2965 7.00 C 11343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 850.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4346 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 16 sheets defined 62.6% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1399 through 1406 Processing helix chain 'A' and resid 1436 through 1458 removed outlier: 4.405A pdb=" N ASP A1454 " --> pdb=" O PHE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1492 Processing helix chain 'A' and resid 1506 through 1534 Processing helix chain 'A' and resid 1535 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1633 removed outlier: 3.746A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.747A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.515A pdb=" N ILE A1648 " --> pdb=" O ILE A1644 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1688 Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.668A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.013A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1814 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.531A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1937 Processing helix chain 'A' and resid 1941 through 1960 removed outlier: 3.701A pdb=" N LEU A1945 " --> pdb=" O ASP A1941 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1987 removed outlier: 4.493A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1990 through 2002 removed outlier: 3.533A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2008 through 2022 Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2080 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 removed outlier: 3.507A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2144 through 2146 No H-bonds generated for 'chain 'A' and resid 2144 through 2146' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2205 through 2210 Processing helix chain 'A' and resid 2221 through 2237 Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2271 removed outlier: 3.628A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2299 Processing helix chain 'A' and resid 2300 through 2305 removed outlier: 5.675A pdb=" N GLN A2303 " --> pdb=" O GLN A2300 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A2304 " --> pdb=" O TRP A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 removed outlier: 3.698A pdb=" N PHE A2346 " --> pdb=" O ILE A2342 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2375 removed outlier: 3.923A pdb=" N SER A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A2375 " --> pdb=" O CYS A2372 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.945A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.170A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 removed outlier: 3.657A pdb=" N LEU A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A2512 " --> pdb=" O GLN A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2588 through 2606 removed outlier: 3.996A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2619 through 2635 Processing helix chain 'A' and resid 2640 through 2656 Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2810 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.795A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2860 Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2899 through 2903 removed outlier: 4.018A pdb=" N ILE A2903 " --> pdb=" O SER A2900 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2961 through 2980 Processing helix chain 'A' and resid 2989 through 3025 Processing helix chain 'A' and resid 3299 through 3334 removed outlier: 4.362A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3357 Processing helix chain 'A' and resid 3365 through 3371 removed outlier: 3.571A pdb=" N TYR A3369 " --> pdb=" O ARG A3365 " (cutoff:3.500A) Processing helix chain 'A' and resid 3372 through 3381 Processing helix chain 'A' and resid 3387 through 3400 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 3.877A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.583A pdb=" N PHE A3457 " --> pdb=" O ASP A3454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3454 through 3458' Processing helix chain 'A' and resid 3462 through 3467 Processing helix chain 'A' and resid 3506 through 3512 Processing helix chain 'A' and resid 3521 through 3537 Processing helix chain 'A' and resid 3538 through 3573 Processing helix chain 'A' and resid 3593 through 3605 Processing helix chain 'A' and resid 3607 through 3618 Processing helix chain 'A' and resid 3619 through 3639 removed outlier: 3.539A pdb=" N GLY A3636 " --> pdb=" O LEU A3632 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A3637 " --> pdb=" O GLU A3633 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 4.029A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A3659 " --> pdb=" O ARG A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3708 Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.660A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3768 Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3808 removed outlier: 3.587A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3835 Processing helix chain 'A' and resid 3843 through 3846 removed outlier: 3.750A pdb=" N MET A3846 " --> pdb=" O ASN A3843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3843 through 3846' Processing helix chain 'A' and resid 3847 through 3860 removed outlier: 4.367A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3902 through 3914 Processing helix chain 'A' and resid 3921 through 3943 removed outlier: 3.708A pdb=" N VAL A3926 " --> pdb=" O GLY A3922 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.635A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4061 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.572A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1386 through 1387 Processing sheet with id=AA2, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 4.273A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1579 " --> pdb=" O ILE A1596 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1596 " --> pdb=" O ILE A1579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1879 removed outlier: 3.509A pdb=" N THR A1886 " --> pdb=" O ILE A1879 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.302A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 5.750A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A2417 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AA8, first strand: chain 'A' and resid 2514 through 2516 Processing sheet with id=AA9, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB1, first strand: chain 'A' and resid 2888 through 2891 removed outlier: 3.825A pdb=" N PHE A2889 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A2891 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.485A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.088A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER A3498 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A3407 " --> pdb=" O SER A3498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3478 through 3481 removed outlier: 3.634A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3811 through 3813 removed outlier: 6.016A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3813 removed outlier: 6.016A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4021 through 4024 removed outlier: 4.219A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A4023 " --> pdb=" O VAL A4027 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A4027 " --> pdb=" O ILE A4023 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 3063 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: 4.50 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5349 1.34 - 1.46: 3142 1.46 - 1.58: 9416 1.58 - 1.70: 11 1.70 - 1.82: 121 Bond restraints: 18039 Sorted by residual: bond pdb=" C VAL A2441 " pdb=" N GLY A2442 " ideal model delta sigma weight residual 1.332 1.343 -0.010 5.00e-03 4.00e+04 4.26e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" CA VAL A3946 " pdb=" CB VAL A3946 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 1.93e+00 bond pdb=" C4 ADP A4104 " pdb=" C5 ADP A4104 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" CB ILE A1896 " pdb=" CG2 ILE A1896 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 ... (remaining 18034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 23718 1.68 - 3.36: 588 3.36 - 5.05: 108 5.05 - 6.73: 41 6.73 - 8.41: 12 Bond angle restraints: 24467 Sorted by residual: angle pdb=" N ALA A2838 " pdb=" CA ALA A2838 " pdb=" C ALA A2838 " ideal model delta sigma weight residual 114.56 109.48 5.08 1.27e+00 6.20e-01 1.60e+01 angle pdb=" C TRP A1398 " pdb=" N ASP A1399 " pdb=" CA ASP A1399 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N GLU A3331 " pdb=" CA GLU A3331 " pdb=" CB GLU A3331 " ideal model delta sigma weight residual 110.39 117.15 -6.76 1.75e+00 3.27e-01 1.49e+01 angle pdb=" C VAL A1448 " pdb=" N GLN A1449 " pdb=" CA GLN A1449 " ideal model delta sigma weight residual 120.29 115.75 4.54 1.42e+00 4.96e-01 1.02e+01 angle pdb=" N ILE A1465 " pdb=" CA ILE A1465 " pdb=" C ILE A1465 " ideal model delta sigma weight residual 111.91 109.16 2.75 8.90e-01 1.26e+00 9.57e+00 ... (remaining 24462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.18: 9771 20.18 - 40.37: 843 40.37 - 60.55: 92 60.55 - 80.73: 23 80.73 - 100.92: 8 Dihedral angle restraints: 10737 sinusoidal: 4063 harmonic: 6674 Sorted by residual: dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 -167.54 -100.92 1 2.00e+01 2.50e-03 2.85e+01 dihedral pdb=" CA CYS A2220 " pdb=" C CYS A2220 " pdb=" N SER A2221 " pdb=" CA SER A2221 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ILE A1841 " pdb=" C ILE A1841 " pdb=" N GLY A1842 " pdb=" CA GLY A1842 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2596 0.078 - 0.156: 236 0.156 - 0.234: 11 0.234 - 0.312: 2 0.312 - 0.390: 1 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB ILE A1765 " pdb=" CA ILE A1765 " pdb=" CG1 ILE A1765 " pdb=" CG2 ILE A1765 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE A2071 " pdb=" CA ILE A2071 " pdb=" CG1 ILE A2071 " pdb=" CG2 ILE A2071 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU A3760 " pdb=" CB LEU A3760 " pdb=" CD1 LEU A3760 " pdb=" CD2 LEU A3760 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2843 not shown) Planarity restraints: 3061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1399 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ASP A1399 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A1399 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A1400 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1772 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A1773 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1773 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1773 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A3900 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A3901 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A3901 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A3901 " -0.024 5.00e-02 4.00e+02 ... (remaining 3058 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3522 2.77 - 3.30: 17706 3.30 - 3.83: 30464 3.83 - 4.37: 32459 4.37 - 4.90: 55647 Nonbonded interactions: 139798 Sorted by model distance: nonbonded pdb=" OG1 THR A2767 " pdb=" O1A ADP A4103 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A3642 " pdb=" OD2 ASP A3691 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A1966 " pdb=" OD2 ASP A2010 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP A2540 " pdb=" OG SER A2904 " model vdw 2.244 3.040 nonbonded pdb=" O LYS A1686 " pdb=" OG SER A1690 " model vdw 2.245 3.040 ... (remaining 139793 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18039 Z= 0.167 Angle : 0.680 8.412 24467 Z= 0.345 Chirality : 0.046 0.390 2846 Planarity : 0.004 0.058 3061 Dihedral : 14.954 100.916 6391 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2232 helix: 0.99 (0.14), residues: 1330 sheet: -0.17 (0.40), residues: 182 loop : -1.54 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2624 TYR 0.012 0.001 TYR A1538 PHE 0.017 0.002 PHE A1620 TRP 0.022 0.002 TRP A1607 HIS 0.007 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00372 (18039) covalent geometry : angle 0.67995 (24467) hydrogen bonds : bond 0.11271 ( 1036) hydrogen bonds : angle 5.13181 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.687 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 1678 MET cc_start: 0.8169 (mmp) cc_final: 0.7950 (mmp) REVERT: A 2167 ASN cc_start: 0.8711 (p0) cc_final: 0.7987 (p0) REVERT: A 2235 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 2485 PHE cc_start: 0.7853 (t80) cc_final: 0.7623 (t80) REVERT: A 2501 ASN cc_start: 0.8155 (p0) cc_final: 0.7634 (p0) REVERT: A 2570 ILE cc_start: 0.8429 (mt) cc_final: 0.8037 (mt) REVERT: A 2600 TYR cc_start: 0.8000 (t80) cc_final: 0.7302 (t80) REVERT: A 2623 THR cc_start: 0.8727 (p) cc_final: 0.8416 (p) REVERT: A 2732 MET cc_start: 0.3644 (mmp) cc_final: 0.2267 (mmt) REVERT: A 2738 MET cc_start: 0.8399 (ptm) cc_final: 0.7980 (ptm) REVERT: A 2927 GLN cc_start: 0.9353 (tp40) cc_final: 0.8801 (tp-100) REVERT: A 3685 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 3698 MET cc_start: 0.8542 (tmm) cc_final: 0.7870 (tpt) REVERT: A 3849 SER cc_start: 0.9453 (m) cc_final: 0.9224 (p) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1320 time to fit residues: 56.6158 Evaluate side-chains 204 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.0030 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1593 ASN A1840 GLN ** A2282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.132270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106042 restraints weight = 54314.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104248 restraints weight = 51181.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105285 restraints weight = 40867.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105483 restraints weight = 30293.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105676 restraints weight = 29571.364| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 18039 Z= 0.281 Angle : 0.737 9.626 24467 Z= 0.377 Chirality : 0.045 0.226 2846 Planarity : 0.005 0.074 3061 Dihedral : 6.269 107.989 2478 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.16 % Allowed : 9.48 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2232 helix: 1.19 (0.14), residues: 1344 sheet: -0.43 (0.38), residues: 187 loop : -1.60 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2620 TYR 0.016 0.002 TYR A2991 PHE 0.031 0.002 PHE A2592 TRP 0.023 0.002 TRP A2084 HIS 0.013 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00637 (18039) covalent geometry : angle 0.73726 (24467) hydrogen bonds : bond 0.04247 ( 1036) hydrogen bonds : angle 4.57914 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.769 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: A 1717 ASN cc_start: 0.8129 (m110) cc_final: 0.7888 (m110) REVERT: A 1754 TYR cc_start: 0.8683 (m-10) cc_final: 0.8479 (m-10) REVERT: A 2493 LYS cc_start: 0.7383 (pttm) cc_final: 0.6945 (pttm) REVERT: A 2501 ASN cc_start: 0.7962 (p0) cc_final: 0.7458 (p0) REVERT: A 2570 ILE cc_start: 0.8236 (mt) cc_final: 0.7968 (mt) REVERT: A 2623 THR cc_start: 0.9144 (p) cc_final: 0.8673 (t) REVERT: A 2732 MET cc_start: 0.3712 (mmp) cc_final: 0.2674 (mmt) REVERT: A 2738 MET cc_start: 0.8722 (ptm) cc_final: 0.8136 (ptm) REVERT: A 2927 GLN cc_start: 0.9047 (tp40) cc_final: 0.8577 (tp-100) REVERT: A 3391 LEU cc_start: 0.7570 (mt) cc_final: 0.7364 (pp) REVERT: A 3698 MET cc_start: 0.8650 (tmm) cc_final: 0.8008 (tmm) REVERT: A 3849 SER cc_start: 0.9196 (m) cc_final: 0.8973 (p) outliers start: 3 outliers final: 2 residues processed: 247 average time/residue: 0.1339 time to fit residues: 51.6788 Evaluate side-chains 195 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2068 GLN ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN A4035 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.137594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109748 restraints weight = 54676.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109268 restraints weight = 39105.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110760 restraints weight = 31062.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110610 restraints weight = 23074.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111216 restraints weight = 24182.605| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18039 Z= 0.139 Angle : 0.581 8.097 24467 Z= 0.296 Chirality : 0.042 0.232 2846 Planarity : 0.004 0.068 3061 Dihedral : 6.021 107.922 2478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.18), residues: 2232 helix: 1.63 (0.14), residues: 1335 sheet: -0.31 (0.38), residues: 183 loop : -1.49 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2624 TYR 0.015 0.001 TYR A1538 PHE 0.020 0.001 PHE A1620 TRP 0.015 0.001 TRP A2084 HIS 0.006 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00308 (18039) covalent geometry : angle 0.58113 (24467) hydrogen bonds : bond 0.03681 ( 1036) hydrogen bonds : angle 4.16736 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.702 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 1717 ASN cc_start: 0.8097 (m110) cc_final: 0.7875 (m110) REVERT: A 2426 MET cc_start: 0.8478 (mmm) cc_final: 0.8258 (tpp) REVERT: A 2501 ASN cc_start: 0.7948 (p0) cc_final: 0.7647 (p0) REVERT: A 2570 ILE cc_start: 0.8596 (mt) cc_final: 0.8263 (mt) REVERT: A 2732 MET cc_start: 0.3063 (mmp) cc_final: 0.2374 (mmt) REVERT: A 2738 MET cc_start: 0.8621 (ptm) cc_final: 0.8388 (ptm) REVERT: A 3698 MET cc_start: 0.8491 (tmm) cc_final: 0.8119 (tmm) REVERT: A 3849 SER cc_start: 0.9417 (m) cc_final: 0.9177 (p) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1404 time to fit residues: 59.5770 Evaluate side-chains 200 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.110253 restraints weight = 54490.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109054 restraints weight = 45379.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.110067 restraints weight = 36270.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110373 restraints weight = 27427.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110484 restraints weight = 26029.598| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18039 Z= 0.167 Angle : 0.605 7.738 24467 Z= 0.307 Chirality : 0.042 0.269 2846 Planarity : 0.004 0.050 3061 Dihedral : 5.968 109.856 2478 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2232 helix: 1.69 (0.14), residues: 1336 sheet: -0.35 (0.38), residues: 183 loop : -1.49 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2336 TYR 0.032 0.001 TYR A2345 PHE 0.019 0.001 PHE A1620 TRP 0.026 0.001 TRP A2084 HIS 0.008 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00379 (18039) covalent geometry : angle 0.60458 (24467) hydrogen bonds : bond 0.03660 ( 1036) hydrogen bonds : angle 4.15983 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.671 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: A 1717 ASN cc_start: 0.8207 (m110) cc_final: 0.7937 (m110) REVERT: A 2426 MET cc_start: 0.8553 (mmm) cc_final: 0.8312 (tpp) REVERT: A 2493 LYS cc_start: 0.7495 (pttm) cc_final: 0.7133 (pttm) REVERT: A 2501 ASN cc_start: 0.7926 (p0) cc_final: 0.7623 (p0) REVERT: A 2570 ILE cc_start: 0.8471 (mt) cc_final: 0.8159 (mt) REVERT: A 2623 THR cc_start: 0.9170 (p) cc_final: 0.8662 (t) REVERT: A 2732 MET cc_start: 0.3125 (mmp) cc_final: 0.2145 (mmt) REVERT: A 2738 MET cc_start: 0.8780 (ptm) cc_final: 0.8196 (ptm) REVERT: A 2741 HIS cc_start: 0.7539 (m-70) cc_final: 0.7286 (m170) REVERT: A 2927 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8265 (tp-100) REVERT: A 3384 LEU cc_start: 0.8410 (mt) cc_final: 0.8207 (mt) REVERT: A 3698 MET cc_start: 0.8508 (tmm) cc_final: 0.7987 (tmm) REVERT: A 3849 SER cc_start: 0.9315 (m) cc_final: 0.9084 (p) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1323 time to fit residues: 52.1541 Evaluate side-chains 197 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111164 restraints weight = 54249.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110907 restraints weight = 41530.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111893 restraints weight = 32877.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111392 restraints weight = 28723.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111609 restraints weight = 26505.292| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18039 Z= 0.130 Angle : 0.571 7.008 24467 Z= 0.289 Chirality : 0.042 0.244 2846 Planarity : 0.003 0.071 3061 Dihedral : 5.845 106.806 2478 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2232 helix: 1.84 (0.14), residues: 1338 sheet: -0.23 (0.38), residues: 183 loop : -1.45 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4075 TYR 0.017 0.001 TYR A2600 PHE 0.027 0.001 PHE A1450 TRP 0.024 0.001 TRP A2084 HIS 0.006 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00290 (18039) covalent geometry : angle 0.57068 (24467) hydrogen bonds : bond 0.03402 ( 1036) hydrogen bonds : angle 4.00239 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.803 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 1717 ASN cc_start: 0.8086 (m110) cc_final: 0.7832 (m110) REVERT: A 2426 MET cc_start: 0.8398 (mmm) cc_final: 0.8187 (tpp) REVERT: A 2501 ASN cc_start: 0.7987 (p0) cc_final: 0.7679 (p0) REVERT: A 2570 ILE cc_start: 0.8493 (mt) cc_final: 0.8200 (mt) REVERT: A 2623 THR cc_start: 0.9105 (p) cc_final: 0.8618 (t) REVERT: A 2732 MET cc_start: 0.2975 (mmp) cc_final: 0.2134 (mmt) REVERT: A 2927 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8298 (tp-100) REVERT: A 3331 GLU cc_start: 0.8323 (pp20) cc_final: 0.8001 (pp20) REVERT: A 3384 LEU cc_start: 0.8366 (mt) cc_final: 0.7720 (pp) REVERT: A 3698 MET cc_start: 0.8598 (tmm) cc_final: 0.8167 (tmm) REVERT: A 3849 SER cc_start: 0.9338 (m) cc_final: 0.9113 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1332 time to fit residues: 56.0112 Evaluate side-chains 200 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 191 optimal weight: 0.0670 chunk 218 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1442 GLN ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1891 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.108480 restraints weight = 54161.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108089 restraints weight = 38017.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109456 restraints weight = 30827.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109361 restraints weight = 22791.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109523 restraints weight = 23066.906| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18039 Z= 0.122 Angle : 0.565 7.054 24467 Z= 0.282 Chirality : 0.041 0.288 2846 Planarity : 0.003 0.057 3061 Dihedral : 5.760 104.899 2478 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2232 helix: 1.93 (0.14), residues: 1339 sheet: -0.17 (0.39), residues: 183 loop : -1.39 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2624 TYR 0.013 0.001 TYR A2571 PHE 0.021 0.001 PHE A2704 TRP 0.024 0.001 TRP A2084 HIS 0.005 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00275 (18039) covalent geometry : angle 0.56459 (24467) hydrogen bonds : bond 0.03342 ( 1036) hydrogen bonds : angle 3.91907 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.637 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 1717 ASN cc_start: 0.8018 (m110) cc_final: 0.7786 (m110) REVERT: A 2501 ASN cc_start: 0.8031 (p0) cc_final: 0.7583 (p0) REVERT: A 2552 ARG cc_start: 0.8461 (ptt90) cc_final: 0.8079 (ptt-90) REVERT: A 2570 ILE cc_start: 0.8580 (mt) cc_final: 0.8216 (mt) REVERT: A 2623 THR cc_start: 0.9119 (p) cc_final: 0.8644 (t) REVERT: A 2732 MET cc_start: 0.3298 (mmp) cc_final: 0.2639 (mmp) REVERT: A 2927 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8354 (tp-100) REVERT: A 3402 ASP cc_start: 0.8126 (m-30) cc_final: 0.7901 (m-30) REVERT: A 3698 MET cc_start: 0.8411 (tmm) cc_final: 0.7887 (tpt) REVERT: A 3849 SER cc_start: 0.9409 (m) cc_final: 0.9185 (p) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1301 time to fit residues: 55.3504 Evaluate side-chains 197 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 177 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110149 restraints weight = 54183.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109523 restraints weight = 40888.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.110997 restraints weight = 31067.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110704 restraints weight = 25239.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.111244 restraints weight = 24576.524| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18039 Z= 0.141 Angle : 0.597 11.293 24467 Z= 0.298 Chirality : 0.042 0.236 2846 Planarity : 0.004 0.054 3061 Dihedral : 5.764 105.620 2478 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2232 helix: 1.87 (0.14), residues: 1339 sheet: -0.24 (0.39), residues: 183 loop : -1.39 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4075 TYR 0.012 0.001 TYR A2571 PHE 0.017 0.001 PHE A1620 TRP 0.022 0.001 TRP A2084 HIS 0.006 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00320 (18039) covalent geometry : angle 0.59657 (24467) hydrogen bonds : bond 0.03423 ( 1036) hydrogen bonds : angle 4.02079 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.743 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: A 1717 ASN cc_start: 0.8116 (m110) cc_final: 0.7895 (m110) REVERT: A 2501 ASN cc_start: 0.7974 (p0) cc_final: 0.7544 (p0) REVERT: A 2552 ARG cc_start: 0.8460 (ptt90) cc_final: 0.8054 (ptt-90) REVERT: A 2570 ILE cc_start: 0.8601 (mt) cc_final: 0.8240 (mt) REVERT: A 2623 THR cc_start: 0.9173 (p) cc_final: 0.8669 (t) REVERT: A 2732 MET cc_start: 0.3270 (mmp) cc_final: 0.2499 (mmt) REVERT: A 2927 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8339 (tp-100) REVERT: A 3402 ASP cc_start: 0.7912 (m-30) cc_final: 0.7668 (m-30) REVERT: A 3698 MET cc_start: 0.8590 (tmm) cc_final: 0.8061 (tmm) REVERT: A 3849 SER cc_start: 0.9391 (m) cc_final: 0.9167 (p) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1392 time to fit residues: 57.0679 Evaluate side-chains 198 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 22 optimal weight: 0.5980 chunk 179 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.137571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.109784 restraints weight = 54055.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109436 restraints weight = 36801.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110303 restraints weight = 29021.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.110382 restraints weight = 25883.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110519 restraints weight = 23369.295| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18039 Z= 0.121 Angle : 0.597 8.975 24467 Z= 0.297 Chirality : 0.042 0.244 2846 Planarity : 0.004 0.053 3061 Dihedral : 5.715 104.244 2478 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.18), residues: 2232 helix: 1.92 (0.14), residues: 1340 sheet: -0.19 (0.38), residues: 183 loop : -1.34 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2624 TYR 0.017 0.001 TYR A2571 PHE 0.018 0.001 PHE A1620 TRP 0.023 0.001 TRP A2084 HIS 0.005 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00270 (18039) covalent geometry : angle 0.59710 (24467) hydrogen bonds : bond 0.03359 ( 1036) hydrogen bonds : angle 3.96883 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.717 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 1717 ASN cc_start: 0.8046 (m110) cc_final: 0.7826 (m110) REVERT: A 2501 ASN cc_start: 0.7938 (p0) cc_final: 0.7485 (p0) REVERT: A 2522 LYS cc_start: 0.8893 (tptp) cc_final: 0.8680 (tptp) REVERT: A 2552 ARG cc_start: 0.8446 (ptt90) cc_final: 0.8116 (ptt-90) REVERT: A 2600 TYR cc_start: 0.7491 (t80) cc_final: 0.6916 (t80) REVERT: A 2623 THR cc_start: 0.9147 (p) cc_final: 0.8674 (t) REVERT: A 2732 MET cc_start: 0.3545 (mmp) cc_final: 0.2780 (mmt) REVERT: A 2738 MET cc_start: 0.8567 (ptm) cc_final: 0.8062 (ptm) REVERT: A 2927 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8356 (tp-100) REVERT: A 3384 LEU cc_start: 0.8405 (mt) cc_final: 0.7693 (pp) REVERT: A 3698 MET cc_start: 0.8565 (tmm) cc_final: 0.8115 (tmm) REVERT: A 3849 SER cc_start: 0.9368 (m) cc_final: 0.9144 (p) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1371 time to fit residues: 57.1295 Evaluate side-chains 199 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 chunk 153 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN A4064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107708 restraints weight = 54003.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107599 restraints weight = 38084.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108670 restraints weight = 29881.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108022 restraints weight = 27845.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108330 restraints weight = 25486.976| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18039 Z= 0.163 Angle : 0.633 9.375 24467 Z= 0.317 Chirality : 0.044 0.352 2846 Planarity : 0.004 0.049 3061 Dihedral : 5.805 105.719 2478 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2232 helix: 1.84 (0.14), residues: 1340 sheet: -0.25 (0.39), residues: 183 loop : -1.38 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2624 TYR 0.011 0.001 TYR A2571 PHE 0.017 0.002 PHE A2669 TRP 0.020 0.001 TRP A2084 HIS 0.007 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00371 (18039) covalent geometry : angle 0.63298 (24467) hydrogen bonds : bond 0.03532 ( 1036) hydrogen bonds : angle 4.07151 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.593 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: A 1717 ASN cc_start: 0.8070 (m110) cc_final: 0.7846 (m110) REVERT: A 2501 ASN cc_start: 0.7915 (p0) cc_final: 0.7610 (p0) REVERT: A 2522 LYS cc_start: 0.8869 (tptp) cc_final: 0.8633 (tptp) REVERT: A 2552 ARG cc_start: 0.8410 (ptt90) cc_final: 0.8070 (ptt-90) REVERT: A 2570 ILE cc_start: 0.8618 (mt) cc_final: 0.8168 (mt) REVERT: A 2600 TYR cc_start: 0.7695 (t80) cc_final: 0.6805 (t80) REVERT: A 2623 THR cc_start: 0.9116 (p) cc_final: 0.8616 (t) REVERT: A 2732 MET cc_start: 0.3611 (mmp) cc_final: 0.2809 (mmp) REVERT: A 2927 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8392 (tp-100) REVERT: A 3384 LEU cc_start: 0.8428 (mt) cc_final: 0.7718 (pp) REVERT: A 3698 MET cc_start: 0.8603 (tmm) cc_final: 0.8110 (tmm) REVERT: A 3849 SER cc_start: 0.9373 (m) cc_final: 0.9145 (p) outliers start: 1 outliers final: 1 residues processed: 257 average time/residue: 0.1270 time to fit residues: 51.6252 Evaluate side-chains 195 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 177 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 ASN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3323 ASN A3685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104869 restraints weight = 55108.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104237 restraints weight = 37616.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105454 restraints weight = 33393.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105213 restraints weight = 26902.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105561 restraints weight = 27908.684| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18039 Z= 0.224 Angle : 0.707 10.978 24467 Z= 0.358 Chirality : 0.046 0.365 2846 Planarity : 0.004 0.051 3061 Dihedral : 6.047 110.069 2478 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2232 helix: 1.55 (0.14), residues: 1345 sheet: -0.44 (0.38), residues: 182 loop : -1.49 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3342 TYR 0.054 0.002 TYR A1758 PHE 0.025 0.002 PHE A2592 TRP 0.024 0.002 TRP A1607 HIS 0.010 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00514 (18039) covalent geometry : angle 0.70747 (24467) hydrogen bonds : bond 0.03930 ( 1036) hydrogen bonds : angle 4.30609 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.652 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 1775 LEU cc_start: 0.7614 (tp) cc_final: 0.7397 (tp) REVERT: A 2368 PHE cc_start: 0.6706 (m-80) cc_final: 0.6408 (m-80) REVERT: A 2501 ASN cc_start: 0.7934 (p0) cc_final: 0.7475 (p0) REVERT: A 2552 ARG cc_start: 0.8474 (ptt90) cc_final: 0.8161 (ptt-90) REVERT: A 2570 ILE cc_start: 0.8565 (mt) cc_final: 0.8159 (mt) REVERT: A 2623 THR cc_start: 0.9140 (p) cc_final: 0.8866 (p) REVERT: A 2732 MET cc_start: 0.3593 (mmp) cc_final: 0.2593 (mmp) REVERT: A 2927 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8441 (tp-100) REVERT: A 3384 LEU cc_start: 0.8403 (mt) cc_final: 0.7692 (pp) REVERT: A 3698 MET cc_start: 0.8720 (tmm) cc_final: 0.8195 (tmm) REVERT: A 3849 SER cc_start: 0.9436 (m) cc_final: 0.9218 (p) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1336 time to fit residues: 53.1912 Evaluate side-chains 189 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN A4035 GLN A4064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.136569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.108007 restraints weight = 54490.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107878 restraints weight = 37643.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109007 restraints weight = 30857.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108783 restraints weight = 24380.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109158 restraints weight = 24050.804| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18039 Z= 0.131 Angle : 0.631 8.453 24467 Z= 0.316 Chirality : 0.043 0.295 2846 Planarity : 0.004 0.048 3061 Dihedral : 5.890 106.385 2478 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2232 helix: 1.77 (0.14), residues: 1339 sheet: -0.30 (0.39), residues: 183 loop : -1.40 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2624 TYR 0.017 0.001 TYR A2571 PHE 0.023 0.001 PHE A1450 TRP 0.022 0.001 TRP A2084 HIS 0.005 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00293 (18039) covalent geometry : angle 0.63085 (24467) hydrogen bonds : bond 0.03494 ( 1036) hydrogen bonds : angle 4.08675 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.42 seconds wall clock time: 53 minutes 28.32 seconds (3208.32 seconds total)