Starting phenix.real_space_refine on Sun Mar 24 03:36:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqh_10551/03_2024/6tqh_10551_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 8 5.49 5 S 92 5.16 5 C 12620 2.51 5 N 3384 2.21 5 O 3778 1.98 5 H 19793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 32": "OD1" <-> "OD2" Residue "A ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 263": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 447": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 463": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 772": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 773": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 790": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 816": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 838": "OD1" <-> "OD2" Residue "A ARG 847": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 865": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 866": "OD1" <-> "OD2" Residue "F ARG 463": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 511": "OE1" <-> "OE2" Residue "F GLU 517": "OE1" <-> "OE2" Residue "F ASP 519": "OD1" <-> "OD2" Residue "F ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 772": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 773": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 790": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 816": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 847": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 865": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 463": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 511": "OE1" <-> "OE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C ASP 519": "OD1" <-> "OD2" Residue "C ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 772": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 773": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 790": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 816": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 847": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 865": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 263": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 447": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 463": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 772": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 773": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 790": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 816": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 838": "OD1" <-> "OD2" Residue "B ARG 847": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 865": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 866": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "F" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6486 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6487 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "B" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.06, per 1000 atoms: 0.43 Number of scatterers: 39677 At special positions: 0 Unit cell: (120.91, 116.39, 142.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 92 16.00 P 8 15.00 O 3778 8.00 N 3384 7.00 C 12620 6.00 H 19793 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.69 Conformation dependent library (CDL) restraints added in 4.1 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 43.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 23 removed outlier: 3.934A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 43 removed outlier: 4.255A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.690A pdb=" N ALA A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 removed outlier: 4.078A pdb=" N ILE A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.512A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 removed outlier: 3.644A pdb=" N LYS A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 147 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 149 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP A 151 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 154 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.034A pdb=" N SER A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 256 through 268 removed outlier: 5.715A pdb=" N ASP A 260 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.585A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.559A pdb=" N GLU A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.675A pdb=" N LYS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.944A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 503 removed outlier: 4.837A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.535A pdb=" N LEU A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 4.254A pdb=" N LYS A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 644 through 662 removed outlier: 3.864A pdb=" N THR A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 679 removed outlier: 3.608A pdb=" N LEU A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 693 through 714 Proline residue: A 697 - end of helix removed outlier: 3.717A pdb=" N GLU A 701 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 703 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 707 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 710 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 729 removed outlier: 4.394A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 745 through 752 removed outlier: 5.427A pdb=" N ARG A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 774 No H-bonds generated for 'chain 'A' and resid 771 through 774' Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 822 through 825 No H-bonds generated for 'chain 'A' and resid 822 through 825' Processing helix chain 'A' and resid 830 through 837 removed outlier: 3.569A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 851 through 854 No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 856 through 862 removed outlier: 4.226A pdb=" N THR A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 471 No H-bonds generated for 'chain 'F' and resid 468 through 471' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 522 through 535 Processing helix chain 'F' and resid 549 through 560 removed outlier: 4.515A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 568 No H-bonds generated for 'chain 'F' and resid 566 through 568' Processing helix chain 'F' and resid 625 through 627 No H-bonds generated for 'chain 'F' and resid 625 through 627' Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 644 through 659 removed outlier: 3.859A pdb=" N PHE F 649 " --> pdb=" O SER F 645 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 655 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 671 No H-bonds generated for 'chain 'F' and resid 669 through 671' Processing helix chain 'F' and resid 673 through 680 Processing helix chain 'F' and resid 686 through 691 Processing helix chain 'F' and resid 693 through 714 Proline residue: F 697 - end of helix removed outlier: 4.725A pdb=" N VAL F 703 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 707 " --> pdb=" O HIS F 704 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA F 710 " --> pdb=" O ALA F 707 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE F 714 " --> pdb=" O GLY F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 731 Processing helix chain 'F' and resid 737 through 752 removed outlier: 3.604A pdb=" N LEU F 743 " --> pdb=" O LEU F 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS F 746 " --> pdb=" O ALA F 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 782 removed outlier: 4.190A pdb=" N ALA F 776 " --> pdb=" O ARG F 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 806 Processing helix chain 'F' and resid 816 through 818 No H-bonds generated for 'chain 'F' and resid 816 through 818' Processing helix chain 'F' and resid 822 through 826 Processing helix chain 'F' and resid 829 through 836 Processing helix chain 'F' and resid 840 through 844 Processing helix chain 'F' and resid 851 through 862 removed outlier: 3.693A pdb=" N LYS F 855 " --> pdb=" O ILE F 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 500 through 504 Processing helix chain 'C' and resid 522 through 535 Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.515A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 625 through 627 No H-bonds generated for 'chain 'C' and resid 625 through 627' Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 644 through 659 removed outlier: 3.859A pdb=" N PHE C 649 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 671 No H-bonds generated for 'chain 'C' and resid 669 through 671' Processing helix chain 'C' and resid 673 through 680 Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 693 through 714 Proline residue: C 697 - end of helix removed outlier: 4.725A pdb=" N VAL C 703 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 707 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 710 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 714 " --> pdb=" O GLY C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 Processing helix chain 'C' and resid 737 through 752 removed outlier: 3.604A pdb=" N LEU C 743 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS C 746 " --> pdb=" O ALA C 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 782 removed outlier: 4.189A pdb=" N ALA C 776 " --> pdb=" O ARG C 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 806 Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 822 through 826 Processing helix chain 'C' and resid 829 through 836 Processing helix chain 'C' and resid 840 through 844 Processing helix chain 'C' and resid 851 through 862 removed outlier: 3.693A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 removed outlier: 3.934A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 4.254A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.689A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 80 removed outlier: 4.079A pdb=" N ILE B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.511A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.644A pdb=" N LYS B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 147 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 149 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 154 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 159 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 199 through 205 removed outlier: 4.034A pdb=" N SER B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 256 through 268 removed outlier: 5.716A pdb=" N ASP B 260 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 268 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.586A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.559A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.676A pdb=" N LYS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.945A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 503 removed outlier: 4.837A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.535A pdb=" N LEU B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 4.253A pdb=" N LYS B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 560 " --> pdb=" O TRP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 569 No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 644 through 662 removed outlier: 3.864A pdb=" N THR B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 661 " --> pdb=" O HIS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.608A pdb=" N LEU B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 693 through 714 Proline residue: B 697 - end of helix removed outlier: 3.718A pdb=" N GLU B 701 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 703 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 707 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 710 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 729 removed outlier: 4.395A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 745 through 752 removed outlier: 5.427A pdb=" N ARG B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 774 No H-bonds generated for 'chain 'B' and resid 771 through 774' Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 793 through 807 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 822 through 825 No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 830 through 837 removed outlier: 3.568A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 851 through 854 No H-bonds generated for 'chain 'B' and resid 851 through 854' Processing helix chain 'B' and resid 856 through 862 removed outlier: 4.227A pdb=" N THR B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 removed outlier: 3.521A pdb=" N ILE A 98 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.346A pdb=" N ILE A 135 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.826A pdb=" N SER A 369 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 251 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 221 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 253 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 252 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA A 342 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 254 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR A 344 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 509 through 513 removed outlier: 6.452A pdb=" N VAL F 539 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 485 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 541 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS F 591 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA F 542 " --> pdb=" O LYS F 591 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 593 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET F 631 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 509 through 513 removed outlier: 6.453A pdb=" N VAL C 539 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL C 485 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 541 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 591 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 542 " --> pdb=" O LYS C 591 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 593 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET C 631 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.522A pdb=" N ILE B 98 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.345A pdb=" N ILE B 135 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.826A pdb=" N SER B 369 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER B 251 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE B 221 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 253 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL B 252 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 342 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 254 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B 344 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.63 Time building geometry restraints manager: 35.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19767 1.02 - 1.21: 30 1.21 - 1.41: 8227 1.41 - 1.61: 11899 1.61 - 1.81: 166 Bond restraints: 40089 Sorted by residual: bond pdb=" C ARG B 865 " pdb=" N ASP B 866 " ideal model delta sigma weight residual 1.331 1.554 -0.223 1.38e-02 5.25e+03 2.60e+02 bond pdb=" C ARG A 865 " pdb=" N ASP A 866 " ideal model delta sigma weight residual 1.331 1.553 -0.222 1.38e-02 5.25e+03 2.59e+02 bond pdb=" O5D NAD B 901 " pdb=" PN NAD B 901 " ideal model delta sigma weight residual 1.637 1.777 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O5D NAD A 902 " pdb=" PN NAD A 902 " ideal model delta sigma weight residual 1.637 1.776 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O5D NAD A 901 " pdb=" PN NAD A 901 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 40084 not shown) Histogram of bond angle deviations from ideal: 72.24 - 84.84: 18 84.84 - 97.44: 13 97.44 - 110.04: 34138 110.04 - 122.64: 33168 122.64 - 135.24: 5311 Bond angle restraints: 72648 Sorted by residual: angle pdb=" CG2 THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 108.00 72.24 35.76 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CG2 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 108.00 73.55 34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" OG1 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 75.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 109.00 77.12 31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CA THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 77.61 31.39 3.00e+00 1.11e-01 1.10e+02 ... (remaining 72643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16926 17.98 - 35.96: 1593 35.96 - 53.94: 351 53.94 - 71.92: 122 71.92 - 89.90: 19 Dihedral angle restraints: 19011 sinusoidal: 10416 harmonic: 8595 Sorted by residual: dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta harmonic sigma weight residual 180.00 147.04 32.96 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA SER B 416 " pdb=" C SER B 416 " pdb=" N LEU B 417 " pdb=" CA LEU B 417 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ILE A 405 " pdb=" C ILE A 405 " pdb=" N GLY A 406 " pdb=" CA GLY A 406 " ideal model delta harmonic sigma weight residual 180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 19008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3023 0.109 - 0.217: 109 0.217 - 0.326: 10 0.326 - 0.435: 0 0.435 - 0.544: 4 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CB THR A 27 " pdb=" CA THR A 27 " pdb=" OG1 THR A 27 " pdb=" CG2 THR A 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB THR B 27 " pdb=" CA THR B 27 " pdb=" OG1 THR B 27 " pdb=" CG2 THR B 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CB THR B 616 " pdb=" CA THR B 616 " pdb=" OG1 THR B 616 " pdb=" CG2 THR B 616 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.32e+00 ... (remaining 3143 not shown) Planarity restraints: 5992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 628 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 628 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.038 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 112 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.031 5.00e-02 4.00e+02 ... (remaining 5989 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 214 1.83 - 2.52: 37628 2.52 - 3.21: 125395 3.21 - 3.91: 164041 3.91 - 4.60: 272436 Nonbonded interactions: 599714 Sorted by model distance: nonbonded pdb=" HE1 HIS A 737 " pdb="FE FE A 903 " model vdw 1.137 1.790 nonbonded pdb=" HE1 HIS B 737 " pdb="FE FE B 903 " model vdw 1.140 1.790 nonbonded pdb="HH12 ARG A 579 " pdb=" O TYR A 581 " model vdw 1.465 1.850 nonbonded pdb="HH12 ARG B 579 " pdb=" O TYR B 581 " model vdw 1.466 1.850 nonbonded pdb=" O GLU A 63 " pdb=" HH TYR B 848 " model vdw 1.509 1.850 ... (remaining 599709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 71 through 869 or resid 901 through 903)) selection = (chain 'B' and (resid 1 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name HA2 or name HA3)) or resid 435 through 869 or resid 901 thr \ ough 903)) } ncs_group { reference = (chain 'C' and (resid 451 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name \ HB2 or name HB3 or name HD21 or name HD22)) or resid 717 through 869)) selection = chain 'F' } 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: 1.070 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: 0.560 Extract box with map and model: 6.030 Check model and map are aligned: 0.640 Set scattering table: 0.340 Process input model: 131.520 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 144.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.013 0.223 20296 Z= 0.850 Angle : 0.924 15.110 27558 Z= 0.455 Chirality : 0.057 0.544 3146 Planarity : 0.005 0.065 3542 Dihedral : 14.919 89.897 7580 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.45 % Allowed : 3.38 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.11), residues: 2568 helix: -4.81 (0.06), residues: 1254 sheet: -3.96 (0.21), residues: 332 loop : -3.39 (0.16), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 424 HIS 0.006 0.001 HIS F 704 PHE 0.017 0.002 PHE C 763 TYR 0.013 0.001 TYR C 867 ARG 0.004 0.001 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 320 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8306 (ttm) cc_final: 0.7993 (ttm) REVERT: F 565 HIS cc_start: 0.7411 (m-70) cc_final: 0.6721 (m-70) REVERT: F 820 VAL cc_start: 0.7003 (t) cc_final: 0.6422 (t) REVERT: B 472 ASP cc_start: 0.7613 (t70) cc_final: 0.7340 (t0) REVERT: B 550 ASP cc_start: 0.8218 (m-30) cc_final: 0.7960 (m-30) outliers start: 30 outliers final: 10 residues processed: 344 average time/residue: 0.8686 time to fit residues: 437.5564 Evaluate side-chains 181 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 868 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 155 GLN A 677 GLN A 754 ASN ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 479 HIS ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20296 Z= 0.186 Angle : 0.589 10.846 27558 Z= 0.303 Chirality : 0.054 1.431 3146 Planarity : 0.005 0.059 3542 Dihedral : 9.334 88.525 2994 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.16 % Allowed : 8.21 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.13), residues: 2568 helix: -3.58 (0.09), residues: 1292 sheet: -3.50 (0.23), residues: 320 loop : -2.41 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 453 HIS 0.005 0.001 HIS F 781 PHE 0.021 0.001 PHE C 714 TYR 0.010 0.001 TYR B 848 ARG 0.004 0.001 ARG F 773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 MET cc_start: 0.8426 (ttm) cc_final: 0.8081 (ttm) REVERT: F 565 HIS cc_start: 0.7241 (m-70) cc_final: 0.6864 (m-70) REVERT: F 592 MET cc_start: 0.8774 (tpt) cc_final: 0.8347 (tpt) REVERT: F 741 ASN cc_start: 0.5949 (m110) cc_final: 0.5662 (m110) REVERT: F 848 TYR cc_start: 0.7427 (t80) cc_final: 0.7206 (t80) REVERT: F 858 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8554 (mm) REVERT: C 558 MET cc_start: 0.8803 (mmm) cc_final: 0.8553 (mmm) REVERT: B 443 THR cc_start: 0.9247 (m) cc_final: 0.8962 (p) REVERT: B 472 ASP cc_start: 0.7450 (t70) cc_final: 0.7161 (t0) REVERT: B 550 ASP cc_start: 0.7962 (m-30) cc_final: 0.7649 (m-30) outliers start: 24 outliers final: 15 residues processed: 214 average time/residue: 0.7349 time to fit residues: 249.6974 Evaluate side-chains 183 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 852 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 479 HIS A 716 ASN F 479 HIS ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 716 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 20296 Z= 0.417 Angle : 0.674 10.917 27558 Z= 0.353 Chirality : 0.055 1.385 3146 Planarity : 0.005 0.093 3542 Dihedral : 8.812 88.968 2990 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.15), residues: 2568 helix: -2.46 (0.12), residues: 1272 sheet: -3.26 (0.25), residues: 330 loop : -1.74 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 453 HIS 0.006 0.002 HIS A 139 PHE 0.019 0.001 PHE A 714 TYR 0.014 0.001 TYR B 259 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8740 (ttm) cc_final: 0.8422 (ttm) REVERT: F 672 ASP cc_start: 0.7252 (m-30) cc_final: 0.7025 (m-30) REVERT: F 848 TYR cc_start: 0.8304 (t80) cc_final: 0.7655 (t80) REVERT: F 858 LEU cc_start: 0.9189 (mm) cc_final: 0.8909 (mm) REVERT: C 592 MET cc_start: 0.8729 (tmm) cc_final: 0.8360 (tpp) REVERT: C 630 ASP cc_start: 0.8440 (m-30) cc_final: 0.8159 (m-30) REVERT: C 852 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8714 (t) REVERT: B 407 ASP cc_start: 0.7219 (t70) cc_final: 0.6826 (t70) REVERT: B 472 ASP cc_start: 0.7759 (t70) cc_final: 0.7477 (t0) REVERT: B 550 ASP cc_start: 0.8006 (m-30) cc_final: 0.7798 (m-30) outliers start: 21 outliers final: 13 residues processed: 182 average time/residue: 0.6789 time to fit residues: 197.3148 Evaluate side-chains 159 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN F 618 GLN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20296 Z= 0.325 Angle : 0.586 10.993 27558 Z= 0.306 Chirality : 0.054 1.418 3146 Planarity : 0.004 0.060 3542 Dihedral : 8.167 89.627 2985 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.35 % Allowed : 12.32 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.16), residues: 2568 helix: -1.84 (0.13), residues: 1276 sheet: -3.12 (0.25), residues: 334 loop : -1.44 (0.22), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 453 HIS 0.004 0.001 HIS A 70 PHE 0.014 0.001 PHE C 714 TYR 0.018 0.001 TYR A 409 ARG 0.003 0.000 ARG F 700 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8713 (ttm) cc_final: 0.8432 (ttm) REVERT: F 848 TYR cc_start: 0.8547 (t80) cc_final: 0.7910 (t80) REVERT: C 558 MET cc_start: 0.8942 (mmm) cc_final: 0.8708 (mmm) REVERT: C 630 ASP cc_start: 0.8423 (m-30) cc_final: 0.8149 (m-30) REVERT: C 852 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (t) REVERT: B 389 MET cc_start: 0.8716 (mmm) cc_final: 0.8486 (mmm) REVERT: B 407 ASP cc_start: 0.7286 (t70) cc_final: 0.6897 (t70) REVERT: B 443 THR cc_start: 0.9426 (m) cc_final: 0.9138 (p) REVERT: B 472 ASP cc_start: 0.7775 (t70) cc_final: 0.7497 (t0) REVERT: B 550 ASP cc_start: 0.7961 (m-30) cc_final: 0.7750 (m-30) outliers start: 28 outliers final: 21 residues processed: 169 average time/residue: 0.7053 time to fit residues: 191.6817 Evaluate side-chains 153 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 725 MET Chi-restraints excluded: chain F residue 767 ASP Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 220 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20296 Z= 0.155 Angle : 0.517 11.051 27558 Z= 0.264 Chirality : 0.053 1.418 3146 Planarity : 0.004 0.055 3542 Dihedral : 7.723 89.607 2984 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.16 % Allowed : 12.95 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.17), residues: 2568 helix: -1.30 (0.14), residues: 1278 sheet: -2.99 (0.26), residues: 338 loop : -1.12 (0.22), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 453 HIS 0.003 0.001 HIS F 723 PHE 0.017 0.001 PHE B 714 TYR 0.010 0.001 TYR F 867 ARG 0.002 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8682 (ttm) cc_final: 0.8388 (ttm) REVERT: C 630 ASP cc_start: 0.8376 (m-30) cc_final: 0.8122 (m-30) REVERT: C 723 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6851 (m-70) REVERT: C 852 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8943 (t) REVERT: B 389 MET cc_start: 0.8659 (mmm) cc_final: 0.8446 (mmm) REVERT: B 407 ASP cc_start: 0.7198 (t70) cc_final: 0.6976 (t70) REVERT: B 443 THR cc_start: 0.9377 (m) cc_final: 0.9120 (p) REVERT: B 472 ASP cc_start: 0.7700 (t70) cc_final: 0.7422 (t0) REVERT: B 550 ASP cc_start: 0.7828 (m-30) cc_final: 0.7579 (m-30) REVERT: B 672 ASP cc_start: 0.7806 (m-30) cc_final: 0.7605 (m-30) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 0.7098 time to fit residues: 189.3349 Evaluate side-chains 154 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20296 Z= 0.274 Angle : 0.552 11.068 27558 Z= 0.286 Chirality : 0.054 1.419 3146 Planarity : 0.004 0.053 3542 Dihedral : 7.556 89.871 2983 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.69 % Allowed : 12.80 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2568 helix: -0.95 (0.14), residues: 1268 sheet: -2.90 (0.26), residues: 338 loop : -0.93 (0.23), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 453 HIS 0.006 0.001 HIS C 561 PHE 0.014 0.001 PHE A 714 TYR 0.014 0.001 TYR A 409 ARG 0.002 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8721 (ttm) cc_final: 0.8450 (ttm) REVERT: A 165 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 350 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: C 630 ASP cc_start: 0.8388 (m-30) cc_final: 0.8127 (m-30) REVERT: B 443 THR cc_start: 0.9443 (m) cc_final: 0.9189 (p) REVERT: B 472 ASP cc_start: 0.7775 (t70) cc_final: 0.7527 (t0) REVERT: B 550 ASP cc_start: 0.7789 (m-30) cc_final: 0.7510 (m-30) outliers start: 35 outliers final: 24 residues processed: 175 average time/residue: 0.7774 time to fit residues: 215.4652 Evaluate side-chains 157 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 845 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 140 optimal weight: 0.0030 chunk 179 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20296 Z= 0.150 Angle : 0.504 11.062 27558 Z= 0.258 Chirality : 0.053 1.425 3146 Planarity : 0.004 0.053 3542 Dihedral : 7.294 88.409 2983 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.26 % Allowed : 13.67 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2568 helix: -0.66 (0.15), residues: 1282 sheet: -2.81 (0.26), residues: 340 loop : -0.75 (0.23), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 453 HIS 0.006 0.001 HIS C 723 PHE 0.014 0.001 PHE B 714 TYR 0.008 0.001 TYR A 409 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8691 (ttm) cc_final: 0.8410 (ttm) REVERT: A 165 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 630 ASP cc_start: 0.8355 (m-30) cc_final: 0.8117 (m-30) REVERT: B 443 THR cc_start: 0.9412 (m) cc_final: 0.9191 (p) REVERT: B 472 ASP cc_start: 0.7680 (t70) cc_final: 0.7433 (t0) REVERT: B 550 ASP cc_start: 0.7726 (m-30) cc_final: 0.7454 (m-30) REVERT: B 592 MET cc_start: 0.8202 (tmm) cc_final: 0.7828 (tpp) outliers start: 26 outliers final: 21 residues processed: 166 average time/residue: 0.7134 time to fit residues: 187.8969 Evaluate side-chains 152 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 845 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 146 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20296 Z= 0.142 Angle : 0.497 11.095 27558 Z= 0.254 Chirality : 0.053 1.427 3146 Planarity : 0.004 0.067 3542 Dihedral : 7.057 86.498 2983 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.97 % Allowed : 14.06 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2568 helix: -0.34 (0.15), residues: 1270 sheet: -2.67 (0.27), residues: 340 loop : -0.61 (0.23), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.005 0.001 HIS C 723 PHE 0.014 0.001 PHE B 714 TYR 0.008 0.001 TYR C 862 ARG 0.007 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8678 (ttm) cc_final: 0.8432 (ttm) REVERT: A 165 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7671 (p0) REVERT: C 630 ASP cc_start: 0.8385 (m-30) cc_final: 0.8150 (m-30) REVERT: B 443 THR cc_start: 0.9399 (m) cc_final: 0.9197 (p) REVERT: B 672 ASP cc_start: 0.7867 (m-30) cc_final: 0.7655 (m-30) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.6953 time to fit residues: 175.1541 Evaluate side-chains 151 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 0.7980 chunk 234 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 215 optimal weight: 0.0670 chunk 227 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20296 Z= 0.133 Angle : 0.491 11.090 27558 Z= 0.251 Chirality : 0.053 1.426 3146 Planarity : 0.003 0.046 3542 Dihedral : 6.846 84.211 2982 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.87 % Allowed : 14.44 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2568 helix: -0.11 (0.15), residues: 1274 sheet: -2.58 (0.27), residues: 338 loop : -0.48 (0.23), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.005 0.001 HIS C 723 PHE 0.014 0.001 PHE B 714 TYR 0.007 0.001 TYR C 862 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8680 (ttm) cc_final: 0.8432 (ttm) REVERT: A 165 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7622 (p0) REVERT: C 630 ASP cc_start: 0.8373 (m-30) cc_final: 0.8112 (m-30) outliers start: 18 outliers final: 16 residues processed: 153 average time/residue: 0.6960 time to fit residues: 169.4720 Evaluate side-chains 150 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20296 Z= 0.196 Angle : 0.512 11.104 27558 Z= 0.264 Chirality : 0.053 1.423 3146 Planarity : 0.004 0.045 3542 Dihedral : 6.863 84.117 2982 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.92 % Allowed : 14.54 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2568 helix: -0.02 (0.15), residues: 1266 sheet: -2.65 (0.26), residues: 348 loop : -0.45 (0.23), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 453 HIS 0.004 0.001 HIS C 723 PHE 0.014 0.001 PHE B 714 TYR 0.008 0.001 TYR C 862 ARG 0.004 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8707 (ttm) cc_final: 0.8459 (ttm) REVERT: A 165 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7660 (p0) REVERT: A 515 GLU cc_start: 0.7628 (mp0) cc_final: 0.7327 (mp0) REVERT: C 630 ASP cc_start: 0.8370 (m-30) cc_final: 0.8146 (m-30) REVERT: B 592 MET cc_start: 0.8222 (tmm) cc_final: 0.7861 (tpp) REVERT: B 631 MET cc_start: 0.9171 (tmm) cc_final: 0.8916 (tmm) outliers start: 19 outliers final: 17 residues processed: 150 average time/residue: 0.7318 time to fit residues: 174.6809 Evaluate side-chains 151 residues out of total 2070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 0.0040 chunk 214 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 0.2980 chunk 207 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 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 = 0.3080 r_free = 0.3080 target = 0.069875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.060711 restraints weight = 151738.965| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.89 r_work: 0.2768 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20296 Z= 0.123 Angle : 0.491 11.119 27558 Z= 0.249 Chirality : 0.053 1.427 3146 Planarity : 0.003 0.047 3542 Dihedral : 6.690 81.428 2982 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.68 % Allowed : 14.78 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2568 helix: 0.19 (0.15), residues: 1272 sheet: -2.46 (0.28), residues: 338 loop : -0.35 (0.23), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.004 0.001 HIS C 723 PHE 0.014 0.001 PHE B 714 TYR 0.007 0.001 TYR B 625 ARG 0.004 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7148.46 seconds wall clock time: 128 minutes 10.24 seconds (7690.24 seconds total)