Starting phenix.real_space_refine on Thu Feb 5 09:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kv7_62587/02_2026/9kv7_62587.map" } resolution = 3.02 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= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10143 2.51 5 N 3105 2.21 5 O 3013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16376 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 712 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Restraints were copied for chains: G, H, I, J, K, B, C, D, E, F, L, P, R, V, X, M, Q, S, U, W, N, O Time building chain proxies: 1.50, per 1000 atoms: 0.09 Number of scatterers: 16376 At special positions: 0 Unit cell: (89.675, 88.62, 148.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3013 8.00 N 3105 7.00 C 10143 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: 1.52 Conformation dependent library (CDL) restraints added in 870.8 milliseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 608 through 629 removed outlier: 6.634A pdb=" N THR A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'G' and resid 572 through 579 Processing helix chain 'G' and resid 582 through 590 Processing helix chain 'G' and resid 593 through 604 Processing helix chain 'G' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR G 626 " --> pdb=" O MET G 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 629 " --> pdb=" O GLY G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 642 Processing helix chain 'G' and resid 644 through 654 Processing helix chain 'H' and resid 572 through 579 Processing helix chain 'H' and resid 582 through 590 Processing helix chain 'H' and resid 593 through 604 Processing helix chain 'H' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR H 626 " --> pdb=" O MET H 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS H 627 " --> pdb=" O ARG H 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 629 " --> pdb=" O GLY H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 642 Processing helix chain 'H' and resid 644 through 654 Processing helix chain 'I' and resid 572 through 579 Processing helix chain 'I' and resid 582 through 590 Processing helix chain 'I' and resid 593 through 604 Processing helix chain 'I' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR I 626 " --> pdb=" O MET I 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS I 627 " --> pdb=" O ARG I 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 629 " --> pdb=" O GLY I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 642 Processing helix chain 'I' and resid 644 through 654 Processing helix chain 'J' and resid 572 through 579 Processing helix chain 'J' and resid 582 through 590 Processing helix chain 'J' and resid 593 through 604 Processing helix chain 'J' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR J 626 " --> pdb=" O MET J 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS J 627 " --> pdb=" O ARG J 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 629 " --> pdb=" O GLY J 625 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 642 Processing helix chain 'J' and resid 644 through 654 Processing helix chain 'K' and resid 572 through 579 Processing helix chain 'K' and resid 582 through 590 Processing helix chain 'K' and resid 593 through 604 Processing helix chain 'K' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR K 626 " --> pdb=" O MET K 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS K 627 " --> pdb=" O ARG K 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA K 629 " --> pdb=" O GLY K 625 " (cutoff:3.500A) Processing helix chain 'K' and resid 630 through 642 Processing helix chain 'K' and resid 644 through 654 Processing helix chain 'B' and resid 572 through 579 Processing helix chain 'B' and resid 582 through 590 Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'C' and resid 572 through 579 Processing helix chain 'C' and resid 582 through 590 Processing helix chain 'C' and resid 593 through 604 Processing helix chain 'C' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR C 626 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 629 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 Processing helix chain 'C' and resid 644 through 654 Processing helix chain 'D' and resid 572 through 579 Processing helix chain 'D' and resid 582 through 590 Processing helix chain 'D' and resid 593 through 604 Processing helix chain 'D' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR D 626 " --> pdb=" O MET D 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS D 627 " --> pdb=" O ARG D 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 629 " --> pdb=" O GLY D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 Processing helix chain 'D' and resid 644 through 654 Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 582 through 590 Processing helix chain 'E' and resid 593 through 604 Processing helix chain 'E' and resid 608 through 629 removed outlier: 6.636A pdb=" N THR E 626 " --> pdb=" O MET E 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS E 627 " --> pdb=" O ARG E 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 629 " --> pdb=" O GLY E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 642 Processing helix chain 'E' and resid 644 through 654 Processing helix chain 'F' and resid 572 through 579 Processing helix chain 'F' and resid 582 through 590 Processing helix chain 'F' and resid 593 through 604 Processing helix chain 'F' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR F 626 " --> pdb=" O MET F 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS F 627 " --> pdb=" O ARG F 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 629 " --> pdb=" O GLY F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 642 Processing helix chain 'F' and resid 644 through 654 Processing helix chain 'L' and resid 572 through 579 Processing helix chain 'L' and resid 582 through 590 Processing helix chain 'L' and resid 593 through 604 Processing helix chain 'L' and resid 608 through 629 removed outlier: 6.634A pdb=" N THR L 626 " --> pdb=" O MET L 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS L 627 " --> pdb=" O ARG L 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA L 629 " --> pdb=" O GLY L 625 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 642 Processing helix chain 'L' and resid 644 through 654 Processing helix chain 'P' and resid 572 through 579 Processing helix chain 'P' and resid 582 through 590 Processing helix chain 'P' and resid 593 through 604 Processing helix chain 'P' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR P 626 " --> pdb=" O MET P 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS P 627 " --> pdb=" O ARG P 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA P 629 " --> pdb=" O GLY P 625 " (cutoff:3.500A) Processing helix chain 'P' and resid 630 through 642 Processing helix chain 'P' and resid 644 through 654 Processing helix chain 'R' and resid 572 through 579 Processing helix chain 'R' and resid 582 through 590 Processing helix chain 'R' and resid 593 through 604 Processing helix chain 'R' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR R 626 " --> pdb=" O MET R 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS R 627 " --> pdb=" O ARG R 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA R 629 " --> pdb=" O GLY R 625 " (cutoff:3.500A) Processing helix chain 'R' and resid 630 through 642 Processing helix chain 'R' and resid 644 through 654 Processing helix chain 'V' and resid 572 through 579 Processing helix chain 'V' and resid 582 through 590 Processing helix chain 'V' and resid 593 through 604 Processing helix chain 'V' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR V 626 " --> pdb=" O MET V 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS V 627 " --> pdb=" O ARG V 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA V 629 " --> pdb=" O GLY V 625 " (cutoff:3.500A) Processing helix chain 'V' and resid 630 through 642 Processing helix chain 'V' and resid 644 through 654 Processing helix chain 'X' and resid 572 through 579 Processing helix chain 'X' and resid 582 through 590 Processing helix chain 'X' and resid 593 through 604 Processing helix chain 'X' and resid 608 through 629 removed outlier: 6.634A pdb=" N THR X 626 " --> pdb=" O MET X 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS X 627 " --> pdb=" O ARG X 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA X 629 " --> pdb=" O GLY X 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 630 through 642 Processing helix chain 'X' and resid 644 through 654 Processing helix chain 'M' and resid 572 through 579 Processing helix chain 'M' and resid 582 through 590 Processing helix chain 'M' and resid 593 through 604 Processing helix chain 'M' and resid 608 through 629 removed outlier: 6.636A pdb=" N THR M 626 " --> pdb=" O MET M 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS M 627 " --> pdb=" O ARG M 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 629 " --> pdb=" O GLY M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 630 through 642 Processing helix chain 'M' and resid 644 through 654 Processing helix chain 'Q' and resid 572 through 579 Processing helix chain 'Q' and resid 582 through 590 Processing helix chain 'Q' and resid 593 through 604 Processing helix chain 'Q' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR Q 626 " --> pdb=" O MET Q 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS Q 627 " --> pdb=" O ARG Q 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA Q 629 " --> pdb=" O GLY Q 625 " (cutoff:3.500A) Processing helix chain 'Q' and resid 630 through 642 Processing helix chain 'Q' and resid 644 through 654 Processing helix chain 'S' and resid 572 through 579 Processing helix chain 'S' and resid 582 through 590 Processing helix chain 'S' and resid 593 through 604 Processing helix chain 'S' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR S 626 " --> pdb=" O MET S 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS S 627 " --> pdb=" O ARG S 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA S 629 " --> pdb=" O GLY S 625 " (cutoff:3.500A) Processing helix chain 'S' and resid 630 through 642 Processing helix chain 'S' and resid 644 through 654 Processing helix chain 'U' and resid 572 through 579 Processing helix chain 'U' and resid 582 through 590 Processing helix chain 'U' and resid 593 through 604 Processing helix chain 'U' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR U 626 " --> pdb=" O MET U 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS U 627 " --> pdb=" O ARG U 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA U 629 " --> pdb=" O GLY U 625 " (cutoff:3.500A) Processing helix chain 'U' and resid 630 through 642 Processing helix chain 'U' and resid 644 through 654 Processing helix chain 'W' and resid 572 through 579 Processing helix chain 'W' and resid 582 through 590 Processing helix chain 'W' and resid 593 through 604 Processing helix chain 'W' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR W 626 " --> pdb=" O MET W 622 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS W 627 " --> pdb=" O ARG W 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA W 629 " --> pdb=" O GLY W 625 " (cutoff:3.500A) Processing helix chain 'W' and resid 630 through 642 Processing helix chain 'W' and resid 644 through 654 Processing helix chain 'N' and resid 572 through 579 Processing helix chain 'N' and resid 582 through 590 Processing helix chain 'N' and resid 593 through 604 Processing helix chain 'N' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR N 626 " --> pdb=" O MET N 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS N 627 " --> pdb=" O ARG N 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA N 629 " --> pdb=" O GLY N 625 " (cutoff:3.500A) Processing helix chain 'N' and resid 630 through 642 Processing helix chain 'N' and resid 644 through 654 Processing helix chain 'O' and resid 572 through 579 Processing helix chain 'O' and resid 582 through 590 Processing helix chain 'O' and resid 593 through 604 Processing helix chain 'O' and resid 608 through 629 removed outlier: 6.635A pdb=" N THR O 626 " --> pdb=" O MET O 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS O 627 " --> pdb=" O ARG O 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA O 629 " --> pdb=" O GLY O 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 630 through 642 Processing helix chain 'O' and resid 644 through 654 1104 hydrogen bonds defined for protein. 3312 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: 2.50 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5704 1.34 - 1.46: 2393 1.46 - 1.57: 8371 1.57 - 1.69: 0 1.69 - 1.80: 161 Bond restraints: 16629 Sorted by residual: bond pdb=" CG LEU F 579 " pdb=" CD2 LEU F 579 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CG LEU M 579 " pdb=" CD2 LEU M 579 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG LEU N 579 " pdb=" CD2 LEU N 579 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG LEU B 579 " pdb=" CD2 LEU B 579 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CG LEU A 579 " pdb=" CD2 LEU A 579 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.16e+00 ... (remaining 16624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 20270 0.93 - 1.86: 1565 1.86 - 2.79: 360 2.79 - 3.72: 0 3.72 - 4.65: 92 Bond angle restraints: 22287 Sorted by residual: angle pdb=" C ASN H 578 " pdb=" N LEU H 579 " pdb=" CA LEU H 579 " ideal model delta sigma weight residual 121.81 117.58 4.23 1.83e+00 2.99e-01 5.35e+00 angle pdb=" C ASN Q 578 " pdb=" N LEU Q 579 " pdb=" CA LEU Q 579 " ideal model delta sigma weight residual 121.81 117.58 4.23 1.83e+00 2.99e-01 5.35e+00 angle pdb=" C ASN S 578 " pdb=" N LEU S 579 " pdb=" CA LEU S 579 " ideal model delta sigma weight residual 121.81 117.58 4.23 1.83e+00 2.99e-01 5.34e+00 angle pdb=" C ASN B 578 " pdb=" N LEU B 579 " pdb=" CA LEU B 579 " ideal model delta sigma weight residual 121.81 117.58 4.23 1.83e+00 2.99e-01 5.34e+00 angle pdb=" C ASN F 578 " pdb=" N LEU F 579 " pdb=" CA LEU F 579 " ideal model delta sigma weight residual 121.81 117.59 4.22 1.83e+00 2.99e-01 5.32e+00 ... (remaining 22282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8837 17.97 - 35.94: 1076 35.94 - 53.91: 184 53.91 - 71.88: 0 71.88 - 89.85: 69 Dihedral angle restraints: 10166 sinusoidal: 4416 harmonic: 5750 Sorted by residual: dihedral pdb=" CG ARG H 588 " pdb=" CD ARG H 588 " pdb=" NE ARG H 588 " pdb=" CZ ARG H 588 " ideal model delta sinusoidal sigma weight residual 180.00 136.64 43.36 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG J 588 " pdb=" CD ARG J 588 " pdb=" NE ARG J 588 " pdb=" CZ ARG J 588 " ideal model delta sinusoidal sigma weight residual 180.00 136.65 43.35 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG B 588 " pdb=" CD ARG B 588 " pdb=" NE ARG B 588 " pdb=" CZ ARG B 588 " ideal model delta sinusoidal sigma weight residual 180.00 136.65 43.35 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 10163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1050 0.023 - 0.047: 827 0.047 - 0.070: 317 0.070 - 0.094: 104 0.094 - 0.117: 71 Chirality restraints: 2369 Sorted by residual: chirality pdb=" CA PRO L 574 " pdb=" N PRO L 574 " pdb=" C PRO L 574 " pdb=" CB PRO L 574 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO C 574 " pdb=" N PRO C 574 " pdb=" C PRO C 574 " pdb=" CB PRO C 574 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA PRO Q 574 " pdb=" N PRO Q 574 " pdb=" C PRO Q 574 " pdb=" CB PRO Q 574 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 2366 not shown) Planarity restraints: 2898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN S 573 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO S 574 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO S 574 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO S 574 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN X 573 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO X 574 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO X 574 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 574 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 573 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO D 574 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 574 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 574 " 0.016 5.00e-02 4.00e+02 ... (remaining 2895 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 501 2.71 - 3.26: 16377 3.26 - 3.80: 26918 3.80 - 4.35: 36036 4.35 - 4.90: 59139 Nonbonded interactions: 138971 Sorted by model distance: nonbonded pdb=" NH2 ARG H 588 " pdb=" OE2 GLU I 611 " model vdw 2.159 3.120 nonbonded pdb=" NH2 ARG I 588 " pdb=" OE2 GLU J 611 " model vdw 2.180 3.120 nonbonded pdb=" OE2 GLU H 611 " pdb=" NH2 ARG X 588 " model vdw 2.207 3.120 nonbonded pdb=" NH2 ARG Q 588 " pdb=" OE2 GLU S 611 " model vdw 2.217 3.120 nonbonded pdb=" NH2 ARG B 588 " pdb=" OE2 GLU C 611 " model vdw 2.218 3.120 ... (remaining 138966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'L' selection = chain 'P' selection = chain 'R' selection = chain 'V' selection = chain 'X' selection = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'N' selection = chain 'O' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.890 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.036 16629 Z= 0.226 Angle : 0.608 4.653 22287 Z= 0.348 Chirality : 0.040 0.117 2369 Planarity : 0.003 0.028 2898 Dihedral : 16.610 89.855 6440 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 0.94 (0.20), residues: 1955 helix: 1.12 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 588 TYR 0.013 0.002 TYR G 604 PHE 0.006 0.002 PHE P 592 TRP 0.007 0.001 TRP M 583 HIS 0.007 0.001 HIS Q 602 Details of bonding type rmsd covalent geometry : bond 0.00547 (16629) covalent geometry : angle 0.60828 (22287) hydrogen bonds : bond 0.17492 ( 1104) hydrogen bonds : angle 7.94321 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 640 GLN cc_start: 0.8637 (mt0) cc_final: 0.8388 (mt0) REVERT: G 578 ASN cc_start: 0.8298 (m-40) cc_final: 0.8027 (m110) REVERT: G 589 LYS cc_start: 0.9153 (mmtm) cc_final: 0.8868 (mmtm) REVERT: G 624 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7908 (mm-30) REVERT: H 604 TYR cc_start: 0.9021 (m-80) cc_final: 0.8818 (m-80) REVERT: H 622 MET cc_start: 0.7980 (mtt) cc_final: 0.7760 (mtt) REVERT: I 624 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7991 (mm-30) REVERT: D 578 ASN cc_start: 0.8123 (m-40) cc_final: 0.7911 (m110) REVERT: E 626 THR cc_start: 0.8943 (t) cc_final: 0.8623 (m) REVERT: F 578 ASN cc_start: 0.8294 (m-40) cc_final: 0.8056 (m-40) REVERT: F 589 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8773 (mmtt) REVERT: L 589 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8754 (mmtt) REVERT: P 619 LYS cc_start: 0.8453 (mttt) cc_final: 0.8172 (mttm) REVERT: R 619 LYS cc_start: 0.8316 (mttt) cc_final: 0.8018 (mttm) REVERT: V 582 GLN cc_start: 0.8059 (mp10) cc_final: 0.7699 (mp10) REVERT: X 578 ASN cc_start: 0.8326 (m-40) cc_final: 0.8100 (m110) REVERT: M 599 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7835 (mt-10) REVERT: M 604 TYR cc_start: 0.9019 (m-80) cc_final: 0.8799 (m-80) REVERT: Q 589 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8745 (mmtt) REVERT: Q 599 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7942 (mt-10) REVERT: S 589 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8706 (mmtt) REVERT: S 604 TYR cc_start: 0.8946 (m-80) cc_final: 0.8682 (m-80) REVERT: U 626 THR cc_start: 0.8949 (t) cc_final: 0.8726 (m) REVERT: N 581 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7731 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1574 time to fit residues: 72.9842 Evaluate side-chains 300 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN C 640 GLN D 640 GLN S 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102329 restraints weight = 16724.015| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.21 r_work: 0.2956 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16629 Z= 0.143 Angle : 0.547 5.149 22287 Z= 0.298 Chirality : 0.040 0.111 2369 Planarity : 0.004 0.029 2898 Dihedral : 4.152 14.519 2185 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1955 helix: 1.40 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 652 TYR 0.017 0.002 TYR D 604 PHE 0.005 0.001 PHE O 592 TRP 0.009 0.001 TRP M 583 HIS 0.006 0.001 HIS D 649 Details of bonding type rmsd covalent geometry : bond 0.00323 (16629) covalent geometry : angle 0.54746 (22287) hydrogen bonds : bond 0.04590 ( 1104) hydrogen bonds : angle 5.92619 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: G 604 TYR cc_start: 0.9037 (m-80) cc_final: 0.8684 (m-80) REVERT: G 624 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8054 (mm-30) REVERT: H 622 MET cc_start: 0.8197 (mtt) cc_final: 0.7908 (mtt) REVERT: E 626 THR cc_start: 0.8782 (t) cc_final: 0.8533 (m) REVERT: F 578 ASN cc_start: 0.8505 (m-40) cc_final: 0.8246 (m-40) REVERT: L 589 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8660 (mmtt) REVERT: P 624 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8142 (mm-30) REVERT: R 578 ASN cc_start: 0.8225 (m110) cc_final: 0.8006 (m-40) REVERT: R 619 LYS cc_start: 0.8406 (mttt) cc_final: 0.8115 (mttm) REVERT: V 578 ASN cc_start: 0.8613 (m-40) cc_final: 0.8382 (m110) REVERT: X 582 GLN cc_start: 0.8510 (mp10) cc_final: 0.8253 (mp10) REVERT: Q 599 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8209 (mt-10) REVERT: Q 601 ASP cc_start: 0.8926 (t0) cc_final: 0.8681 (t0) REVERT: S 589 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8606 (mmtt) REVERT: U 601 ASP cc_start: 0.8840 (t0) cc_final: 0.8599 (t0) REVERT: N 581 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7946 (ttp-170) REVERT: O 578 ASN cc_start: 0.8243 (m-40) cc_final: 0.7961 (m110) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1403 time to fit residues: 61.7366 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** V 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 648 ASN S 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101428 restraints weight = 17054.922| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.32 r_work: 0.2939 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16629 Z= 0.124 Angle : 0.503 5.323 22287 Z= 0.276 Chirality : 0.038 0.120 2369 Planarity : 0.003 0.029 2898 Dihedral : 3.997 13.355 2185 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.17 % Allowed : 9.50 % Favored : 90.33 % 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 are not related in a simple way. whole: 1.58 (0.20), residues: 1955 helix: 1.65 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.37 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 652 TYR 0.017 0.002 TYR D 604 PHE 0.004 0.001 PHE N 592 TRP 0.006 0.001 TRP A 583 HIS 0.004 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00273 (16629) covalent geometry : angle 0.50291 (22287) hydrogen bonds : bond 0.04174 ( 1104) hydrogen bonds : angle 5.55439 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 604 TYR cc_start: 0.9012 (m-80) cc_final: 0.8706 (m-80) REVERT: G 624 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8065 (mm-30) REVERT: H 622 MET cc_start: 0.8229 (mtt) cc_final: 0.7947 (mtt) REVERT: J 578 ASN cc_start: 0.8431 (m110) cc_final: 0.8224 (m110) REVERT: J 603 ASP cc_start: 0.8900 (m-30) cc_final: 0.8695 (m-30) REVERT: E 626 THR cc_start: 0.8740 (t) cc_final: 0.8446 (m) REVERT: F 578 ASN cc_start: 0.8603 (m-40) cc_final: 0.8328 (m-40) REVERT: L 589 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8643 (mmtt) REVERT: P 624 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8140 (mm-30) REVERT: P 650 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.6044 (tp) REVERT: V 578 ASN cc_start: 0.8610 (m-40) cc_final: 0.8342 (m110) REVERT: X 582 GLN cc_start: 0.8452 (mp10) cc_final: 0.8178 (mp10) REVERT: Q 599 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8277 (mt-10) REVERT: S 571 HIS cc_start: 0.7500 (m90) cc_final: 0.7298 (m90) REVERT: S 604 TYR cc_start: 0.8895 (m-80) cc_final: 0.8480 (m-80) REVERT: W 626 THR cc_start: 0.8728 (t) cc_final: 0.8523 (m) REVERT: N 581 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7901 (ttp-170) REVERT: O 578 ASN cc_start: 0.8133 (m-40) cc_final: 0.7789 (m110) outliers start: 3 outliers final: 2 residues processed: 299 average time/residue: 0.1383 time to fit residues: 61.1069 Evaluate side-chains 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 607 ASP Chi-restraints excluded: chain P residue 607 ASP Chi-restraints excluded: chain P residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 29 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103459 restraints weight = 16920.116| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.33 r_work: 0.2965 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16629 Z= 0.110 Angle : 0.483 5.336 22287 Z= 0.265 Chirality : 0.037 0.115 2369 Planarity : 0.003 0.033 2898 Dihedral : 3.939 12.868 2185 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 10.98 % Favored : 88.96 % 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 are not related in a simple way. whole: 1.78 (0.20), residues: 1955 helix: 1.79 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 652 TYR 0.017 0.002 TYR D 604 PHE 0.003 0.001 PHE N 592 TRP 0.006 0.001 TRP M 583 HIS 0.003 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00237 (16629) covalent geometry : angle 0.48300 (22287) hydrogen bonds : bond 0.03850 ( 1104) hydrogen bonds : angle 5.39743 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: G 604 TYR cc_start: 0.9028 (m-80) cc_final: 0.8744 (m-80) REVERT: G 624 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8015 (mm-30) REVERT: H 578 ASN cc_start: 0.8493 (m110) cc_final: 0.8259 (m110) REVERT: H 622 MET cc_start: 0.8183 (mtt) cc_final: 0.7908 (mtt) REVERT: J 578 ASN cc_start: 0.8423 (m110) cc_final: 0.8215 (m110) REVERT: C 640 GLN cc_start: 0.8519 (mt0) cc_final: 0.8258 (mt0) REVERT: E 626 THR cc_start: 0.8712 (t) cc_final: 0.8410 (m) REVERT: F 578 ASN cc_start: 0.8573 (m-40) cc_final: 0.8299 (m-40) REVERT: L 589 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8638 (mmtt) REVERT: P 624 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8088 (mm-30) REVERT: R 578 ASN cc_start: 0.8201 (m110) cc_final: 0.8001 (m-40) REVERT: R 604 TYR cc_start: 0.8966 (m-80) cc_final: 0.8743 (m-80) REVERT: V 578 ASN cc_start: 0.8453 (m-40) cc_final: 0.8246 (m110) REVERT: X 582 GLN cc_start: 0.8495 (mp10) cc_final: 0.8216 (mp10) REVERT: Q 599 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8240 (mt-10) REVERT: S 571 HIS cc_start: 0.7445 (m90) cc_final: 0.7230 (m90) REVERT: S 604 TYR cc_start: 0.8878 (m-80) cc_final: 0.8495 (m-80) REVERT: N 581 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7892 (ttp-170) REVERT: O 578 ASN cc_start: 0.8099 (m-40) cc_final: 0.7748 (m110) outliers start: 1 outliers final: 1 residues processed: 298 average time/residue: 0.1301 time to fit residues: 57.0491 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 630 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102644 restraints weight = 16869.823| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.23 r_work: 0.2934 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16629 Z= 0.146 Angle : 0.518 6.589 22287 Z= 0.283 Chirality : 0.038 0.115 2369 Planarity : 0.004 0.039 2898 Dihedral : 3.912 13.232 2185 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.14 % Allowed : 10.24 % Favored : 88.62 % 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 are not related in a simple way. whole: 1.75 (0.20), residues: 1955 helix: 1.75 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 652 TYR 0.021 0.002 TYR D 604 PHE 0.004 0.001 PHE N 592 TRP 0.006 0.001 TRP P 583 HIS 0.006 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00339 (16629) covalent geometry : angle 0.51805 (22287) hydrogen bonds : bond 0.04342 ( 1104) hydrogen bonds : angle 5.37871 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 0.668 Fit side-chains REVERT: G 604 TYR cc_start: 0.9091 (m-80) cc_final: 0.8791 (m-80) REVERT: G 624 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8058 (mm-30) REVERT: E 626 THR cc_start: 0.8851 (t) cc_final: 0.8578 (m) REVERT: L 589 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8744 (mmtt) REVERT: V 578 ASN cc_start: 0.8608 (m-40) cc_final: 0.8359 (m110) REVERT: V 627 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8305 (mtpp) REVERT: X 582 GLN cc_start: 0.8468 (mp10) cc_final: 0.8234 (mp10) REVERT: Q 599 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8288 (mt-10) REVERT: S 571 HIS cc_start: 0.7483 (m90) cc_final: 0.7281 (m90) REVERT: U 571 HIS cc_start: 0.7733 (m170) cc_final: 0.7420 (m-70) REVERT: N 581 ARG cc_start: 0.8228 (ttt180) cc_final: 0.7897 (ttp-170) REVERT: O 578 ASN cc_start: 0.8236 (m-40) cc_final: 0.7930 (m110) outliers start: 20 outliers final: 2 residues processed: 316 average time/residue: 0.1399 time to fit residues: 64.9964 Evaluate side-chains 292 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102537 restraints weight = 16835.703| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.21 r_work: 0.2953 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16629 Z= 0.139 Angle : 0.509 5.693 22287 Z= 0.278 Chirality : 0.038 0.116 2369 Planarity : 0.004 0.032 2898 Dihedral : 3.915 13.125 2185 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.34 % Allowed : 10.35 % Favored : 89.30 % 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 are not related in a simple way. whole: 1.83 (0.20), residues: 1955 helix: 1.78 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 652 TYR 0.021 0.002 TYR D 604 PHE 0.004 0.001 PHE R 592 TRP 0.006 0.001 TRP O 583 HIS 0.005 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00321 (16629) covalent geometry : angle 0.50921 (22287) hydrogen bonds : bond 0.04196 ( 1104) hydrogen bonds : angle 5.31099 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 292 time to evaluate : 0.735 Fit side-chains REVERT: G 604 TYR cc_start: 0.9087 (m-80) cc_final: 0.8758 (m-80) REVERT: G 624 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8052 (mm-30) REVERT: K 619 LYS cc_start: 0.8431 (mttt) cc_final: 0.8204 (mttm) REVERT: E 626 THR cc_start: 0.8881 (t) cc_final: 0.8335 (m) REVERT: L 589 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8692 (mmtt) REVERT: V 578 ASN cc_start: 0.8633 (m-40) cc_final: 0.8390 (m110) REVERT: X 582 GLN cc_start: 0.8416 (mp10) cc_final: 0.8155 (mp10) REVERT: Q 599 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8263 (mt-10) REVERT: N 581 ARG cc_start: 0.8224 (ttt180) cc_final: 0.7847 (ttp-170) REVERT: O 578 ASN cc_start: 0.8334 (m-40) cc_final: 0.7996 (m110) outliers start: 6 outliers final: 2 residues processed: 296 average time/residue: 0.1348 time to fit residues: 59.3780 Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103134 restraints weight = 16724.037| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.19 r_work: 0.3028 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16629 Z= 0.130 Angle : 0.501 5.543 22287 Z= 0.274 Chirality : 0.038 0.119 2369 Planarity : 0.003 0.034 2898 Dihedral : 3.891 13.000 2185 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.34 % Allowed : 10.98 % Favored : 88.67 % 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 are not related in a simple way. whole: 1.92 (0.20), residues: 1955 helix: 1.85 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 652 TYR 0.020 0.002 TYR D 604 PHE 0.004 0.001 PHE N 592 TRP 0.006 0.001 TRP E 583 HIS 0.005 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00294 (16629) covalent geometry : angle 0.50070 (22287) hydrogen bonds : bond 0.04091 ( 1104) hydrogen bonds : angle 5.23492 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 284 time to evaluate : 0.656 Fit side-chains REVERT: G 604 TYR cc_start: 0.9082 (m-80) cc_final: 0.8754 (m-80) REVERT: G 624 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8018 (mm-30) REVERT: K 619 LYS cc_start: 0.8391 (mttt) cc_final: 0.8148 (mttm) REVERT: E 617 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8435 (mm) REVERT: E 626 THR cc_start: 0.8887 (t) cc_final: 0.8363 (m) REVERT: L 589 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8710 (mmtt) REVERT: L 619 LYS cc_start: 0.8516 (mttm) cc_final: 0.8295 (mmtp) REVERT: P 601 ASP cc_start: 0.8655 (t0) cc_final: 0.8425 (t0) REVERT: V 578 ASN cc_start: 0.8620 (m-40) cc_final: 0.8379 (m110) REVERT: Q 599 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8280 (mt-10) REVERT: S 619 LYS cc_start: 0.8489 (mttm) cc_final: 0.8251 (mmtm) REVERT: N 581 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7832 (ttp-170) REVERT: O 578 ASN cc_start: 0.8388 (m-40) cc_final: 0.8051 (m110) outliers start: 6 outliers final: 3 residues processed: 287 average time/residue: 0.1366 time to fit residues: 58.3958 Evaluate side-chains 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 571 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain P residue 607 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102242 restraints weight = 16863.296| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.21 r_work: 0.3000 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16629 Z= 0.140 Angle : 0.514 5.565 22287 Z= 0.280 Chirality : 0.038 0.116 2369 Planarity : 0.003 0.033 2898 Dihedral : 3.890 13.182 2185 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.23 % Allowed : 10.98 % Favored : 88.79 % 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 are not related in a simple way. whole: 1.90 (0.20), residues: 1955 helix: 1.83 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 652 TYR 0.022 0.002 TYR D 604 PHE 0.004 0.001 PHE N 592 TRP 0.006 0.001 TRP E 583 HIS 0.005 0.001 HIS N 602 Details of bonding type rmsd covalent geometry : bond 0.00323 (16629) covalent geometry : angle 0.51361 (22287) hydrogen bonds : bond 0.04250 ( 1104) hydrogen bonds : angle 5.19930 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.769 Fit side-chains REVERT: G 604 TYR cc_start: 0.9093 (m-80) cc_final: 0.8760 (m-80) REVERT: G 624 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8033 (mm-30) REVERT: K 619 LYS cc_start: 0.8384 (mttt) cc_final: 0.8122 (mttm) REVERT: E 617 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8431 (mm) REVERT: E 626 THR cc_start: 0.8879 (t) cc_final: 0.8377 (m) REVERT: L 589 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8693 (mmtt) REVERT: P 624 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8256 (mm-30) REVERT: V 578 ASN cc_start: 0.8641 (m-40) cc_final: 0.8389 (m110) REVERT: Q 599 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8274 (mt-10) REVERT: U 571 HIS cc_start: 0.7812 (m-70) cc_final: 0.7561 (m-70) REVERT: N 581 ARG cc_start: 0.8209 (ttt180) cc_final: 0.7792 (ttp-170) REVERT: O 578 ASN cc_start: 0.8450 (m-40) cc_final: 0.8117 (m110) outliers start: 4 outliers final: 3 residues processed: 283 average time/residue: 0.1354 time to fit residues: 56.3937 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 571 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain P residue 607 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 54 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 640 GLN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** R 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103633 restraints weight = 16752.032| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.31 r_work: 0.2973 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16629 Z= 0.112 Angle : 0.487 5.105 22287 Z= 0.266 Chirality : 0.037 0.113 2369 Planarity : 0.003 0.030 2898 Dihedral : 3.854 13.013 2185 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 10.98 % Favored : 88.79 % 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 are not related in a simple way. whole: 2.11 (0.20), residues: 1955 helix: 1.99 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 623 TYR 0.019 0.002 TYR D 604 PHE 0.003 0.001 PHE X 592 TRP 0.007 0.001 TRP E 583 HIS 0.004 0.001 HIS N 602 Details of bonding type rmsd covalent geometry : bond 0.00243 (16629) covalent geometry : angle 0.48707 (22287) hydrogen bonds : bond 0.03774 ( 1104) hydrogen bonds : angle 5.04008 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 283 time to evaluate : 0.578 Fit side-chains REVERT: G 578 ASN cc_start: 0.8607 (m110) cc_final: 0.8389 (m110) REVERT: G 604 TYR cc_start: 0.9038 (m-80) cc_final: 0.8741 (m-80) REVERT: G 624 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8151 (mm-30) REVERT: H 578 ASN cc_start: 0.8577 (m110) cc_final: 0.8354 (m110) REVERT: K 619 LYS cc_start: 0.8326 (mttt) cc_final: 0.8067 (mttm) REVERT: E 617 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8373 (mm) REVERT: E 626 THR cc_start: 0.8828 (t) cc_final: 0.8322 (m) REVERT: L 589 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8670 (mmtt) REVERT: P 624 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8318 (mm-30) REVERT: R 604 TYR cc_start: 0.8992 (m-80) cc_final: 0.8787 (m-80) REVERT: R 619 LYS cc_start: 0.8319 (mmtp) cc_final: 0.8075 (mmtm) REVERT: V 578 ASN cc_start: 0.8605 (m-40) cc_final: 0.8373 (m110) REVERT: Q 599 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8269 (mt-10) REVERT: U 571 HIS cc_start: 0.7899 (m-70) cc_final: 0.7662 (m-70) REVERT: N 581 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7825 (ttp-170) REVERT: N 619 LYS cc_start: 0.8447 (mttm) cc_final: 0.8165 (mttt) REVERT: O 578 ASN cc_start: 0.8338 (m-40) cc_final: 0.8016 (m110) outliers start: 4 outliers final: 3 residues processed: 284 average time/residue: 0.1287 time to fit residues: 54.6572 Evaluate side-chains 282 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 571 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain P residue 607 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 95 optimal weight: 0.0370 chunk 169 optimal weight: 0.0870 chunk 130 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 150 optimal weight: 0.0170 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 640 GLN D 640 GLN L 640 GLN ** M 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108082 restraints weight = 16795.209| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.29 r_work: 0.3070 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16629 Z= 0.090 Angle : 0.465 6.085 22287 Z= 0.254 Chirality : 0.036 0.114 2369 Planarity : 0.003 0.028 2898 Dihedral : 3.807 12.578 2185 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.23 % Allowed : 11.44 % Favored : 88.33 % 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 are not related in a simple way. whole: 2.36 (0.20), residues: 1955 helix: 2.20 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -1.12 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 623 TYR 0.015 0.002 TYR D 604 PHE 0.003 0.000 PHE K 592 TRP 0.008 0.001 TRP O 583 HIS 0.002 0.000 HIS M 649 Details of bonding type rmsd covalent geometry : bond 0.00174 (16629) covalent geometry : angle 0.46523 (22287) hydrogen bonds : bond 0.03215 ( 1104) hydrogen bonds : angle 4.86294 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 288 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: G 604 TYR cc_start: 0.8979 (m-80) cc_final: 0.8736 (m-80) REVERT: G 624 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8159 (mm-30) REVERT: G 627 LYS cc_start: 0.8163 (pttm) cc_final: 0.7787 (mmtt) REVERT: E 617 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8313 (mm) REVERT: E 626 THR cc_start: 0.8795 (t) cc_final: 0.8296 (m) REVERT: F 578 ASN cc_start: 0.8572 (m-40) cc_final: 0.8258 (m-40) REVERT: F 619 LYS cc_start: 0.8526 (mttm) cc_final: 0.8222 (mmtp) REVERT: L 589 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8651 (mmtt) REVERT: P 601 ASP cc_start: 0.8451 (t0) cc_final: 0.8235 (t0) REVERT: P 624 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8245 (mm-30) REVERT: R 624 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8044 (mm-30) REVERT: V 578 ASN cc_start: 0.8516 (m-40) cc_final: 0.8291 (m110) REVERT: V 619 LYS cc_start: 0.8581 (mttm) cc_final: 0.8115 (mttt) REVERT: S 604 TYR cc_start: 0.8837 (m-80) cc_final: 0.8430 (m-80) REVERT: S 619 LYS cc_start: 0.8223 (mttm) cc_final: 0.7974 (mmtm) REVERT: U 571 HIS cc_start: 0.7845 (m-70) cc_final: 0.7608 (m-70) REVERT: N 581 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7793 (ttp-170) REVERT: N 619 LYS cc_start: 0.8320 (mttm) cc_final: 0.8079 (mmtt) REVERT: O 578 ASN cc_start: 0.8119 (m-40) cc_final: 0.7879 (m110) outliers start: 4 outliers final: 3 residues processed: 289 average time/residue: 0.1313 time to fit residues: 56.5067 Evaluate side-chains 278 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain D residue 607 ASP Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain P residue 607 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 640 GLN L 640 GLN S 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107373 restraints weight = 16443.535| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.22 r_work: 0.2962 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16629 Z= 0.147 Angle : 0.531 5.905 22287 Z= 0.289 Chirality : 0.039 0.119 2369 Planarity : 0.004 0.035 2898 Dihedral : 3.820 13.213 2185 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.29 % Allowed : 11.56 % Favored : 88.16 % 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 are not related in a simple way. whole: 2.18 (0.20), residues: 1955 helix: 2.03 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.027 0.002 TYR R 604 PHE 0.004 0.001 PHE N 592 TRP 0.008 0.001 TRP P 583 HIS 0.005 0.001 HIS X 602 Details of bonding type rmsd covalent geometry : bond 0.00339 (16629) covalent geometry : angle 0.53068 (22287) hydrogen bonds : bond 0.04320 ( 1104) hydrogen bonds : angle 4.96390 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3853.62 seconds wall clock time: 67 minutes 13.25 seconds (4033.25 seconds total)