Starting phenix.real_space_refine on Fri Mar 15 16:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/03_2024/6ofe_20043.pdb" } resolution = 3.61 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= 0.004 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: 3 Type Number sf(0) Gaussians C 7740 2.51 5 N 2020 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 20 Chain: "P" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "S" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "A" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 6.45, per 1000 atoms: 0.53 Number of scatterers: 12220 At special positions: 0 Unit cell: (90.915, 90.915, 154.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2460 8.00 N 2020 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA P 49 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS P 66 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.529A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS Q 66 " --> pdb=" O SER Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL R 65 " --> pdb=" O GLN R 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS T 66 " --> pdb=" O SER T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS K 66 " --> pdb=" O SER K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O GLN L 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.527A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS O 66 " --> pdb=" O SER O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS I 66 " --> pdb=" O SER I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA J 49 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN A 77 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN B 77 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN C 77 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2640 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: 3.33 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2180 1.29 - 1.35: 1840 1.35 - 1.41: 1193 1.41 - 1.48: 1867 1.48 - 1.54: 5360 Bond restraints: 12440 Sorted by residual: bond pdb=" C LYS J 37 " pdb=" N PRO J 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.65e+00 bond pdb=" C LYS T 37 " pdb=" N PRO T 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C LYS G 37 " pdb=" N PRO G 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.63e+00 bond pdb=" C LYS C 37 " pdb=" N PRO C 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 bond pdb=" C LYS L 37 " pdb=" N PRO L 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 12435 not shown) Histogram of bond angle deviations from ideal: 102.60 - 108.87: 588 108.87 - 115.14: 6944 115.14 - 121.41: 6883 121.41 - 127.68: 2465 127.68 - 133.95: 60 Bond angle restraints: 16940 Sorted by residual: angle pdb=" NE ARG N 58 " pdb=" CZ ARG N 58 " pdb=" NH1 ARG N 58 " ideal model delta sigma weight residual 121.50 119.93 1.57 1.00e+00 1.00e+00 2.45e+00 angle pdb=" C ILE L 75 " pdb=" N ILE L 76 " pdb=" CA ILE L 76 " ideal model delta sigma weight residual 120.46 122.59 -2.13 1.37e+00 5.33e-01 2.42e+00 angle pdb=" NE ARG J 58 " pdb=" CZ ARG J 58 " pdb=" NH1 ARG J 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.38e+00 angle pdb=" NE ARG P 58 " pdb=" CZ ARG P 58 " pdb=" NH1 ARG P 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.38e+00 angle pdb=" NE ARG D 58 " pdb=" CZ ARG D 58 " pdb=" NH1 ARG D 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.36e+00 ... (remaining 16935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.77: 6306 8.77 - 17.54: 974 17.54 - 26.32: 100 26.32 - 35.09: 80 35.09 - 43.86: 80 Dihedral angle restraints: 7540 sinusoidal: 2880 harmonic: 4660 Sorted by residual: dihedral pdb=" CB LYS R 50 " pdb=" CG LYS R 50 " pdb=" CD LYS R 50 " pdb=" CE LYS R 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.86 -43.86 3 1.50e+01 4.44e-03 7.89e+00 dihedral pdb=" CB LYS G 50 " pdb=" CG LYS G 50 " pdb=" CD LYS G 50 " pdb=" CE LYS G 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.85 -43.85 3 1.50e+01 4.44e-03 7.88e+00 dihedral pdb=" CB LYS F 50 " pdb=" CG LYS F 50 " pdb=" CD LYS F 50 " pdb=" CE LYS F 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.83 -43.83 3 1.50e+01 4.44e-03 7.88e+00 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 588 0.022 - 0.044: 747 0.044 - 0.065: 446 0.065 - 0.087: 139 0.087 - 0.109: 20 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" C PRO I 41 " pdb=" CB PRO I 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA PRO N 41 " pdb=" N PRO N 41 " pdb=" C PRO N 41 " pdb=" CB PRO N 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA PRO S 41 " pdb=" N PRO S 41 " pdb=" C PRO S 41 " pdb=" CB PRO S 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 ... (remaining 1937 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 40 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 41 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 40 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO R 41 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP T 40 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO T 41 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO T 41 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO T 41 " -0.022 5.00e-02 4.00e+02 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4239 2.84 - 3.36: 11891 3.36 - 3.87: 19701 3.87 - 4.39: 24705 4.39 - 4.90: 40716 Nonbonded interactions: 101252 Sorted by model distance: nonbonded pdb=" OD1 ASP T 17 " pdb=" OH TYR T 57 " model vdw 2.325 2.440 nonbonded pdb=" OD1 ASP H 17 " pdb=" OH TYR H 57 " model vdw 2.325 2.440 nonbonded pdb=" OD1 ASP K 17 " pdb=" OH TYR K 57 " model vdw 2.325 2.440 nonbonded pdb=" OD1 ASP P 17 " pdb=" OH TYR P 57 " model vdw 2.325 2.440 nonbonded pdb=" OD1 ASP F 17 " pdb=" OH TYR F 57 " model vdw 2.325 2.440 ... (remaining 101247 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.090 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.006 0.031 12440 Z= 0.374 Angle : 0.633 3.134 16940 Z= 0.358 Chirality : 0.041 0.109 1940 Planarity : 0.005 0.040 2220 Dihedral : 10.068 43.861 4500 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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: -6.24 (0.12), residues: 1520 helix: -3.97 (0.07), residues: 1320 sheet: None (None), residues: 0 loop : -2.59 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP G 5 PHE 0.012 0.002 PHE M 79 TYR 0.009 0.001 TYR D 57 ARG 0.002 0.001 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 47 TYR cc_start: 0.9272 (t80) cc_final: 0.8932 (t80) REVERT: T 15 LYS cc_start: 0.8101 (mttt) cc_final: 0.7744 (tttt) REVERT: T 47 TYR cc_start: 0.9346 (t80) cc_final: 0.9008 (t80) REVERT: K 25 THR cc_start: 0.9286 (m) cc_final: 0.8722 (p) REVERT: K 37 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7937 (tptt) REVERT: K 47 TYR cc_start: 0.9330 (t80) cc_final: 0.9011 (t80) REVERT: K 55 ASN cc_start: 0.8335 (t0) cc_final: 0.8022 (t0) REVERT: L 25 THR cc_start: 0.9141 (m) cc_final: 0.8682 (p) REVERT: L 39 SER cc_start: 0.8964 (m) cc_final: 0.8038 (p) REVERT: L 70 ASP cc_start: 0.8141 (m-30) cc_final: 0.7870 (m-30) REVERT: M 25 THR cc_start: 0.9206 (m) cc_final: 0.8855 (p) REVERT: M 32 ASP cc_start: 0.7748 (m-30) cc_final: 0.7423 (m-30) REVERT: M 39 SER cc_start: 0.9152 (m) cc_final: 0.8521 (p) REVERT: N 39 SER cc_start: 0.9110 (m) cc_final: 0.8397 (p) REVERT: N 47 TYR cc_start: 0.9238 (t80) cc_final: 0.8941 (t80) REVERT: N 55 ASN cc_start: 0.8363 (t0) cc_final: 0.8072 (t0) REVERT: O 39 SER cc_start: 0.8989 (m) cc_final: 0.8053 (p) REVERT: O 52 SER cc_start: 0.8954 (m) cc_final: 0.8700 (p) REVERT: F 37 LYS cc_start: 0.8655 (ttmt) cc_final: 0.7952 (tptp) REVERT: F 39 SER cc_start: 0.8645 (m) cc_final: 0.7821 (m) REVERT: G 37 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7814 (tptt) REVERT: G 39 SER cc_start: 0.8925 (m) cc_final: 0.7319 (m) REVERT: H 37 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7481 (tptt) REVERT: I 37 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7639 (tptt) REVERT: I 57 TYR cc_start: 0.9073 (t80) cc_final: 0.8861 (t80) REVERT: J 37 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7576 (tptt) REVERT: J 55 ASN cc_start: 0.8252 (t0) cc_final: 0.7881 (t0) REVERT: D 24 GLN cc_start: 0.7878 (mp10) cc_final: 0.7666 (mp10) REVERT: D 37 LYS cc_start: 0.8736 (ttmt) cc_final: 0.7633 (tptt) REVERT: A 37 LYS cc_start: 0.8767 (ttmt) cc_final: 0.7670 (tptp) REVERT: B 37 LYS cc_start: 0.8793 (ttmt) cc_final: 0.7831 (tptt) REVERT: C 37 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8088 (tptt) REVERT: E 37 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8153 (tptt) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2373 time to fit residues: 142.6533 Evaluate side-chains 332 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 24 GLN R 63 ASN T 61 GLN T 63 ASN K 63 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 ASN M 24 GLN M 63 ASN N 63 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN J 63 ASN D 24 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 24 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 12440 Z= 0.145 Angle : 0.471 6.327 16940 Z= 0.255 Chirality : 0.033 0.103 1940 Planarity : 0.004 0.023 2220 Dihedral : 3.848 13.187 1680 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.62 % Allowed : 16.54 % Favored : 81.85 % 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: -2.35 (0.17), residues: 1520 helix: -1.13 (0.11), residues: 1380 sheet: None (None), residues: 0 loop : -3.95 (0.41), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 5 PHE 0.010 0.001 PHE N 16 TYR 0.009 0.001 TYR J 57 ARG 0.005 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 351 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 55 ASN cc_start: 0.8481 (t0) cc_final: 0.8166 (t0) REVERT: Q 29 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7742 (mt-10) REVERT: Q 37 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8502 (ttmm) REVERT: T 39 SER cc_start: 0.9251 (m) cc_final: 0.8242 (m) REVERT: T 69 LYS cc_start: 0.8656 (tmtp) cc_final: 0.7475 (tttt) REVERT: K 37 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7979 (tptt) REVERT: K 53 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6460 (mt-10) REVERT: K 55 ASN cc_start: 0.8220 (t0) cc_final: 0.7921 (t0) REVERT: L 25 THR cc_start: 0.9021 (m) cc_final: 0.8764 (p) REVERT: L 55 ASN cc_start: 0.8296 (t0) cc_final: 0.8013 (t0) REVERT: L 70 ASP cc_start: 0.7918 (m-30) cc_final: 0.7705 (m-30) REVERT: O 52 SER cc_start: 0.9000 (m) cc_final: 0.8749 (p) REVERT: O 53 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8339 (mm-30) REVERT: F 24 GLN cc_start: 0.8425 (mp10) cc_final: 0.7953 (mp10) REVERT: F 37 LYS cc_start: 0.8630 (ttmt) cc_final: 0.7927 (tptp) REVERT: F 39 SER cc_start: 0.8650 (m) cc_final: 0.7549 (m) REVERT: G 37 LYS cc_start: 0.8571 (ttmt) cc_final: 0.7860 (tptt) REVERT: G 39 SER cc_start: 0.8831 (m) cc_final: 0.7621 (m) REVERT: H 37 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7356 (tptt) REVERT: I 37 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7762 (tptt) REVERT: I 55 ASN cc_start: 0.8108 (t0) cc_final: 0.7768 (t0) REVERT: J 17 ASP cc_start: 0.7907 (m-30) cc_final: 0.7656 (m-30) REVERT: J 37 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7666 (tptt) REVERT: J 55 ASN cc_start: 0.8057 (t0) cc_final: 0.7788 (t0) REVERT: D 37 LYS cc_start: 0.8655 (ttmt) cc_final: 0.7501 (tptt) REVERT: A 24 GLN cc_start: 0.8341 (mp10) cc_final: 0.7880 (mp10) REVERT: A 33 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8630 (mtpt) REVERT: A 37 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7518 (tptp) REVERT: B 37 LYS cc_start: 0.8671 (ttmt) cc_final: 0.7766 (tptt) REVERT: C 37 LYS cc_start: 0.8737 (ttmt) cc_final: 0.7898 (tptt) REVERT: E 37 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8161 (tptp) REVERT: E 53 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7317 (mm-30) outliers start: 21 outliers final: 5 residues processed: 358 average time/residue: 0.2373 time to fit residues: 120.9739 Evaluate side-chains 311 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 24 GLN N 24 GLN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12440 Z= 0.146 Angle : 0.432 6.606 16940 Z= 0.226 Chirality : 0.033 0.103 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.626 14.280 1680 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.92 % Allowed : 21.08 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.20), residues: 1520 helix: 0.79 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -2.14 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 5 PHE 0.007 0.001 PHE L 16 TYR 0.010 0.001 TYR N 47 ARG 0.004 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 319 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7661 (mt-10) REVERT: T 39 SER cc_start: 0.9231 (m) cc_final: 0.8975 (p) REVERT: T 62 SER cc_start: 0.9380 (t) cc_final: 0.8946 (t) REVERT: K 37 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7836 (tptt) REVERT: K 55 ASN cc_start: 0.8189 (t0) cc_final: 0.7909 (t0) REVERT: L 55 ASN cc_start: 0.8290 (t0) cc_final: 0.8028 (t0) REVERT: M 47 TYR cc_start: 0.9090 (t80) cc_final: 0.8689 (t80) REVERT: O 32 ASP cc_start: 0.7978 (m-30) cc_final: 0.7736 (m-30) REVERT: O 47 TYR cc_start: 0.9109 (t80) cc_final: 0.8894 (t80) REVERT: O 52 SER cc_start: 0.9054 (m) cc_final: 0.8778 (p) REVERT: F 37 LYS cc_start: 0.8623 (ttmt) cc_final: 0.7883 (tptp) REVERT: G 37 LYS cc_start: 0.8520 (ttmt) cc_final: 0.7899 (tptt) REVERT: H 25 THR cc_start: 0.9194 (m) cc_final: 0.8983 (t) REVERT: H 37 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7468 (tptt) REVERT: I 37 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7656 (tptt) REVERT: I 55 ASN cc_start: 0.8060 (t0) cc_final: 0.7731 (t0) REVERT: J 37 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7501 (tptt) REVERT: J 55 ASN cc_start: 0.8095 (t0) cc_final: 0.7835 (t0) REVERT: D 37 LYS cc_start: 0.8716 (ttmt) cc_final: 0.7480 (tptt) REVERT: A 22 ASN cc_start: 0.8099 (p0) cc_final: 0.7858 (p0) REVERT: A 37 LYS cc_start: 0.8628 (ttmt) cc_final: 0.7517 (tptp) REVERT: B 37 LYS cc_start: 0.8712 (ttmt) cc_final: 0.7796 (tptt) REVERT: B 57 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.8909 (t80) REVERT: C 37 LYS cc_start: 0.8876 (ttmt) cc_final: 0.7880 (tptt) REVERT: E 37 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8141 (tptp) outliers start: 25 outliers final: 17 residues processed: 330 average time/residue: 0.2213 time to fit residues: 105.3696 Evaluate side-chains 313 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 295 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.0050 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 63 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 24 GLN M 26 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 55 ASN N 61 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12440 Z= 0.111 Angle : 0.402 5.632 16940 Z= 0.208 Chirality : 0.033 0.099 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.482 14.432 1680 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.62 % Allowed : 23.38 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1520 helix: 1.64 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -1.88 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 5 PHE 0.005 0.001 PHE D 16 TYR 0.008 0.001 TYR N 47 ARG 0.003 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 321 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7669 (mt-10) REVERT: Q 37 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8463 (ttmm) REVERT: T 62 SER cc_start: 0.9353 (t) cc_final: 0.8951 (t) REVERT: K 37 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7847 (tptp) REVERT: K 55 ASN cc_start: 0.8135 (t0) cc_final: 0.7881 (t0) REVERT: L 22 ASN cc_start: 0.7912 (p0) cc_final: 0.7481 (p0) REVERT: M 47 TYR cc_start: 0.9102 (t80) cc_final: 0.8705 (t80) REVERT: O 47 TYR cc_start: 0.9111 (t80) cc_final: 0.8894 (t80) REVERT: O 52 SER cc_start: 0.9122 (m) cc_final: 0.8692 (p) REVERT: F 37 LYS cc_start: 0.8617 (ttmt) cc_final: 0.7826 (tptp) REVERT: G 37 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7990 (tptp) REVERT: H 25 THR cc_start: 0.9155 (m) cc_final: 0.8900 (t) REVERT: H 37 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7508 (tptp) REVERT: I 37 LYS cc_start: 0.8449 (ttmt) cc_final: 0.7641 (tptt) REVERT: I 55 ASN cc_start: 0.7974 (t0) cc_final: 0.7650 (t0) REVERT: J 17 ASP cc_start: 0.7926 (m-30) cc_final: 0.7708 (m-30) REVERT: J 37 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7472 (tptt) REVERT: J 55 ASN cc_start: 0.8063 (t0) cc_final: 0.7658 (t0) REVERT: D 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7568 (tptt) REVERT: A 24 GLN cc_start: 0.8392 (mp10) cc_final: 0.7956 (mp10) REVERT: A 37 LYS cc_start: 0.8619 (ttmt) cc_final: 0.7506 (tptp) REVERT: B 37 LYS cc_start: 0.8690 (ttmt) cc_final: 0.7774 (tptt) REVERT: B 53 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 61 GLN cc_start: 0.8801 (tt0) cc_final: 0.8440 (tt0) REVERT: C 37 LYS cc_start: 0.8732 (ttmt) cc_final: 0.7853 (tptt) REVERT: E 37 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8216 (tptp) REVERT: E 53 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7441 (mm-30) REVERT: E 55 ASN cc_start: 0.8434 (t0) cc_final: 0.8176 (t0) outliers start: 21 outliers final: 14 residues processed: 331 average time/residue: 0.2268 time to fit residues: 108.0660 Evaluate side-chains 315 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 301 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 24 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 55 ASN O 24 GLN I 61 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12440 Z= 0.142 Angle : 0.420 6.011 16940 Z= 0.215 Chirality : 0.034 0.100 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.466 14.109 1680 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.92 % Allowed : 23.69 % Favored : 74.38 % 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: 2.76 (0.21), residues: 1520 helix: 2.18 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.55 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.005 0.001 PHE A 16 TYR 0.008 0.001 TYR R 54 ARG 0.003 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 306 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: R 62 SER cc_start: 0.9167 (t) cc_final: 0.8861 (t) REVERT: T 62 SER cc_start: 0.9352 (t) cc_final: 0.8955 (t) REVERT: K 37 LYS cc_start: 0.8367 (ttmt) cc_final: 0.7815 (tptp) REVERT: K 55 ASN cc_start: 0.8166 (t0) cc_final: 0.7906 (t0) REVERT: M 47 TYR cc_start: 0.9120 (t80) cc_final: 0.8717 (t80) REVERT: N 32 ASP cc_start: 0.7646 (m-30) cc_final: 0.7431 (m-30) REVERT: O 47 TYR cc_start: 0.9135 (t80) cc_final: 0.8926 (t80) REVERT: O 52 SER cc_start: 0.9119 (m) cc_final: 0.8718 (p) REVERT: F 37 LYS cc_start: 0.8592 (ttmt) cc_final: 0.7783 (tptp) REVERT: G 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7971 (tptp) REVERT: H 37 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7504 (tptp) REVERT: I 15 LYS cc_start: 0.8590 (tppp) cc_final: 0.8191 (tptp) REVERT: I 22 ASN cc_start: 0.7976 (p0) cc_final: 0.7610 (t0) REVERT: I 55 ASN cc_start: 0.8026 (t0) cc_final: 0.7716 (t0) REVERT: J 17 ASP cc_start: 0.8003 (m-30) cc_final: 0.7745 (m-30) REVERT: J 37 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7406 (tptt) REVERT: J 55 ASN cc_start: 0.8075 (t0) cc_final: 0.7802 (t0) REVERT: D 37 LYS cc_start: 0.8718 (ttmt) cc_final: 0.7531 (tptt) REVERT: A 24 GLN cc_start: 0.8375 (mp10) cc_final: 0.7984 (mp10) REVERT: A 37 LYS cc_start: 0.8624 (ttmt) cc_final: 0.7494 (tptp) REVERT: B 37 LYS cc_start: 0.8707 (ttmt) cc_final: 0.7755 (tptt) REVERT: B 53 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7630 (mm-30) REVERT: C 37 LYS cc_start: 0.8790 (ttmt) cc_final: 0.7834 (tptt) REVERT: E 37 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8198 (tptp) outliers start: 25 outliers final: 18 residues processed: 318 average time/residue: 0.2447 time to fit residues: 112.3698 Evaluate side-chains 311 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 293 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN P 63 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 24 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN O 24 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12440 Z= 0.153 Angle : 0.424 5.877 16940 Z= 0.218 Chirality : 0.034 0.101 1940 Planarity : 0.003 0.028 2220 Dihedral : 3.469 14.341 1680 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.08 % Allowed : 22.69 % Favored : 74.23 % 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: 3.09 (0.21), residues: 1520 helix: 2.42 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.64 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.005 0.001 PHE A 16 TYR 0.009 0.001 TYR N 47 ARG 0.002 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7652 (mt-10) REVERT: R 62 SER cc_start: 0.9163 (t) cc_final: 0.8848 (t) REVERT: T 62 SER cc_start: 0.9346 (t) cc_final: 0.8953 (t) REVERT: K 37 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7798 (tptp) REVERT: K 55 ASN cc_start: 0.8172 (t0) cc_final: 0.7904 (t0) REVERT: K 57 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8219 (t80) REVERT: L 22 ASN cc_start: 0.7971 (p0) cc_final: 0.7592 (p0) REVERT: M 47 TYR cc_start: 0.9134 (t80) cc_final: 0.8716 (t80) REVERT: O 52 SER cc_start: 0.9121 (m) cc_final: 0.8722 (p) REVERT: F 22 ASN cc_start: 0.8144 (p0) cc_final: 0.7680 (p0) REVERT: F 37 LYS cc_start: 0.8593 (ttmt) cc_final: 0.7777 (tptp) REVERT: G 37 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7972 (tptp) REVERT: H 37 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7513 (tptp) REVERT: I 15 LYS cc_start: 0.8627 (tppp) cc_final: 0.8329 (tptm) REVERT: I 22 ASN cc_start: 0.8009 (p0) cc_final: 0.7650 (t0) REVERT: I 55 ASN cc_start: 0.8077 (t0) cc_final: 0.7766 (t0) REVERT: J 17 ASP cc_start: 0.8067 (m-30) cc_final: 0.7810 (m-30) REVERT: J 37 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7428 (tptt) REVERT: J 53 GLU cc_start: 0.8275 (tp30) cc_final: 0.8044 (mm-30) REVERT: J 55 ASN cc_start: 0.8076 (t0) cc_final: 0.7855 (t0) REVERT: D 37 LYS cc_start: 0.8727 (ttmt) cc_final: 0.7497 (tptt) REVERT: A 24 GLN cc_start: 0.8339 (mp10) cc_final: 0.7977 (mp10) REVERT: A 37 LYS cc_start: 0.8632 (ttmt) cc_final: 0.7482 (tptp) REVERT: B 37 LYS cc_start: 0.8732 (ttmt) cc_final: 0.7747 (tptt) REVERT: B 53 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7599 (mm-30) REVERT: C 37 LYS cc_start: 0.8805 (ttmt) cc_final: 0.7831 (tptt) REVERT: E 37 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8193 (tptp) outliers start: 40 outliers final: 30 residues processed: 328 average time/residue: 0.2255 time to fit residues: 106.6254 Evaluate side-chains 324 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 83 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: P 24 GLN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 55 ASN O 24 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12440 Z= 0.135 Angle : 0.418 5.736 16940 Z= 0.214 Chirality : 0.033 0.099 1940 Planarity : 0.003 0.028 2220 Dihedral : 3.448 14.507 1680 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.85 % Allowed : 23.23 % Favored : 73.92 % 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: 3.30 (0.21), residues: 1520 helix: 2.58 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 5 PHE 0.004 0.001 PHE A 16 TYR 0.010 0.001 TYR D 47 ARG 0.002 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7593 (mt-10) REVERT: R 62 SER cc_start: 0.9259 (t) cc_final: 0.8912 (t) REVERT: T 5 TRP cc_start: 0.8857 (t60) cc_final: 0.8597 (t60) REVERT: T 62 SER cc_start: 0.9421 (t) cc_final: 0.9006 (t) REVERT: K 37 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7755 (tptp) REVERT: K 55 ASN cc_start: 0.8154 (t0) cc_final: 0.7894 (t0) REVERT: K 57 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8258 (t80) REVERT: L 22 ASN cc_start: 0.8050 (p0) cc_final: 0.7645 (p0) REVERT: M 47 TYR cc_start: 0.9131 (t80) cc_final: 0.8720 (t80) REVERT: O 52 SER cc_start: 0.9127 (m) cc_final: 0.8721 (p) REVERT: F 22 ASN cc_start: 0.8220 (p0) cc_final: 0.7677 (p0) REVERT: F 37 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7765 (tptp) REVERT: G 37 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7956 (tptp) REVERT: H 37 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7509 (tptp) REVERT: I 22 ASN cc_start: 0.8044 (p0) cc_final: 0.7716 (t0) REVERT: I 55 ASN cc_start: 0.8045 (t0) cc_final: 0.7761 (t0) REVERT: J 17 ASP cc_start: 0.8034 (m-30) cc_final: 0.7782 (m-30) REVERT: J 37 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7370 (tptt) REVERT: J 53 GLU cc_start: 0.8297 (tp30) cc_final: 0.8043 (mm-30) REVERT: J 55 ASN cc_start: 0.8050 (t0) cc_final: 0.7838 (t0) REVERT: D 37 LYS cc_start: 0.8718 (ttmt) cc_final: 0.7485 (tptt) REVERT: A 24 GLN cc_start: 0.8317 (mp10) cc_final: 0.7925 (mp10) REVERT: A 37 LYS cc_start: 0.8631 (ttmt) cc_final: 0.7473 (tptp) REVERT: B 37 LYS cc_start: 0.8729 (ttmt) cc_final: 0.7744 (tptt) REVERT: B 53 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 37 LYS cc_start: 0.8807 (ttmt) cc_final: 0.7830 (tptt) REVERT: E 37 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8190 (tptp) outliers start: 37 outliers final: 26 residues processed: 326 average time/residue: 0.2239 time to fit residues: 106.4066 Evaluate side-chains 321 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 24 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN O 24 GLN G 24 GLN I 63 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12440 Z= 0.166 Angle : 0.434 5.517 16940 Z= 0.224 Chirality : 0.034 0.103 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.507 15.585 1680 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.92 % Allowed : 23.23 % Favored : 73.85 % 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: 3.36 (0.21), residues: 1520 helix: 2.63 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.75 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 5 PHE 0.004 0.001 PHE C 68 TYR 0.009 0.001 TYR K 57 ARG 0.002 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 303 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7598 (mt-10) REVERT: R 62 SER cc_start: 0.9281 (t) cc_final: 0.8939 (t) REVERT: T 5 TRP cc_start: 0.8875 (t60) cc_final: 0.8582 (t60) REVERT: T 62 SER cc_start: 0.9476 (t) cc_final: 0.9066 (t) REVERT: K 37 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7804 (tptp) REVERT: K 55 ASN cc_start: 0.8197 (t0) cc_final: 0.7923 (t0) REVERT: K 57 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8315 (t80) REVERT: L 22 ASN cc_start: 0.8099 (p0) cc_final: 0.7682 (p0) REVERT: M 24 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: O 52 SER cc_start: 0.9100 (m) cc_final: 0.8713 (p) REVERT: F 22 ASN cc_start: 0.8288 (p0) cc_final: 0.7920 (p0) REVERT: F 37 LYS cc_start: 0.8700 (ttmt) cc_final: 0.7855 (tptp) REVERT: G 37 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8020 (tptp) REVERT: H 37 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7586 (tptp) REVERT: I 22 ASN cc_start: 0.8144 (p0) cc_final: 0.7812 (t0) REVERT: I 55 ASN cc_start: 0.8093 (t0) cc_final: 0.7820 (t0) REVERT: J 17 ASP cc_start: 0.8100 (m-30) cc_final: 0.7827 (m-30) REVERT: J 22 ASN cc_start: 0.8205 (p0) cc_final: 0.7951 (p0) REVERT: J 37 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7413 (tptt) REVERT: J 53 GLU cc_start: 0.8295 (tp30) cc_final: 0.8042 (mm-30) REVERT: J 55 ASN cc_start: 0.8089 (t0) cc_final: 0.7864 (t0) REVERT: D 37 LYS cc_start: 0.8749 (ttmt) cc_final: 0.7501 (tptt) REVERT: A 24 GLN cc_start: 0.8325 (mp10) cc_final: 0.7954 (mp10) REVERT: A 37 LYS cc_start: 0.8622 (ttmt) cc_final: 0.7448 (tptp) REVERT: B 37 LYS cc_start: 0.8719 (ttmt) cc_final: 0.7670 (tptt) REVERT: B 53 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 37 LYS cc_start: 0.8941 (ttmt) cc_final: 0.7826 (tptt) REVERT: E 37 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8152 (tptp) outliers start: 38 outliers final: 31 residues processed: 327 average time/residue: 0.2197 time to fit residues: 104.6425 Evaluate side-chains 331 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 298 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 24 GLN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN O 24 GLN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12440 Z= 0.131 Angle : 0.424 5.954 16940 Z= 0.218 Chirality : 0.034 0.104 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.465 15.073 1680 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.31 % Allowed : 24.08 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.53 (0.21), residues: 1520 helix: 2.76 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 5 PHE 0.004 0.001 PHE A 16 TYR 0.009 0.001 TYR N 47 ARG 0.002 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7571 (mt-10) REVERT: R 62 SER cc_start: 0.9388 (t) cc_final: 0.9071 (t) REVERT: S 5 TRP cc_start: 0.8642 (t60) cc_final: 0.8404 (t60) REVERT: T 5 TRP cc_start: 0.8852 (t60) cc_final: 0.8561 (t60) REVERT: T 62 SER cc_start: 0.9460 (t) cc_final: 0.9053 (t) REVERT: K 37 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7764 (tptp) REVERT: K 55 ASN cc_start: 0.8152 (t0) cc_final: 0.7876 (t0) REVERT: K 57 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8256 (t80) REVERT: L 22 ASN cc_start: 0.8075 (p0) cc_final: 0.7669 (p0) REVERT: M 47 TYR cc_start: 0.9136 (t80) cc_final: 0.8725 (t80) REVERT: O 52 SER cc_start: 0.9105 (m) cc_final: 0.8724 (p) REVERT: F 22 ASN cc_start: 0.8259 (p0) cc_final: 0.7880 (p0) REVERT: F 37 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7838 (tptp) REVERT: G 37 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7920 (tptp) REVERT: H 37 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7540 (tptp) REVERT: I 22 ASN cc_start: 0.8244 (p0) cc_final: 0.7894 (t0) REVERT: I 55 ASN cc_start: 0.8032 (t0) cc_final: 0.7747 (t0) REVERT: J 17 ASP cc_start: 0.8068 (m-30) cc_final: 0.7807 (m-30) REVERT: J 22 ASN cc_start: 0.8151 (p0) cc_final: 0.7894 (p0) REVERT: J 37 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7424 (tptt) REVERT: J 53 GLU cc_start: 0.8345 (tp30) cc_final: 0.8087 (mm-30) REVERT: J 55 ASN cc_start: 0.8039 (t0) cc_final: 0.7833 (t0) REVERT: D 37 LYS cc_start: 0.8748 (ttmt) cc_final: 0.7524 (tptt) REVERT: A 24 GLN cc_start: 0.8298 (mp10) cc_final: 0.7937 (mp10) REVERT: A 37 LYS cc_start: 0.8608 (ttmt) cc_final: 0.7425 (tptp) REVERT: B 37 LYS cc_start: 0.8743 (ttmt) cc_final: 0.7734 (tptt) REVERT: B 53 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 37 LYS cc_start: 0.8925 (ttmt) cc_final: 0.7815 (tptt) REVERT: E 37 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8164 (tptp) outliers start: 30 outliers final: 26 residues processed: 328 average time/residue: 0.2125 time to fit residues: 101.3408 Evaluate side-chains 325 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 55 ASN H 63 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12440 Z= 0.150 Angle : 0.435 5.751 16940 Z= 0.223 Chirality : 0.034 0.102 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.469 15.081 1680 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.38 % Allowed : 24.69 % Favored : 72.92 % 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: 3.66 (0.21), residues: 1520 helix: 2.85 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.78 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.004 0.001 PHE N 16 TYR 0.009 0.001 TYR D 47 ARG 0.002 0.000 ARG J 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 303 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7577 (mt-10) REVERT: R 62 SER cc_start: 0.9262 (t) cc_final: 0.8908 (t) REVERT: S 5 TRP cc_start: 0.8641 (t60) cc_final: 0.8382 (t60) REVERT: T 5 TRP cc_start: 0.8852 (t60) cc_final: 0.8549 (t60) REVERT: T 62 SER cc_start: 0.9446 (t) cc_final: 0.9049 (t) REVERT: K 37 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7769 (tptp) REVERT: K 55 ASN cc_start: 0.8210 (t0) cc_final: 0.7930 (t0) REVERT: K 57 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8216 (t80) REVERT: L 22 ASN cc_start: 0.8075 (p0) cc_final: 0.7652 (p0) REVERT: M 47 TYR cc_start: 0.9148 (t80) cc_final: 0.8743 (t80) REVERT: O 52 SER cc_start: 0.9116 (m) cc_final: 0.8730 (p) REVERT: F 22 ASN cc_start: 0.8174 (p0) cc_final: 0.7739 (p0) REVERT: F 24 GLN cc_start: 0.8302 (mp10) cc_final: 0.7829 (mp10) REVERT: F 37 LYS cc_start: 0.8688 (ttmt) cc_final: 0.7829 (tptp) REVERT: G 37 LYS cc_start: 0.8460 (ttmt) cc_final: 0.7953 (tptp) REVERT: H 37 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7572 (tptp) REVERT: I 22 ASN cc_start: 0.8262 (p0) cc_final: 0.7909 (t0) REVERT: I 55 ASN cc_start: 0.8055 (t0) cc_final: 0.7779 (t0) REVERT: J 17 ASP cc_start: 0.8075 (m-30) cc_final: 0.7798 (m-30) REVERT: J 37 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7413 (tptt) REVERT: J 53 GLU cc_start: 0.8362 (tp30) cc_final: 0.8100 (mm-30) REVERT: J 55 ASN cc_start: 0.8072 (t0) cc_final: 0.7853 (t0) REVERT: D 37 LYS cc_start: 0.8785 (ttmt) cc_final: 0.7522 (tptt) REVERT: A 24 GLN cc_start: 0.8293 (mp10) cc_final: 0.7944 (mp10) REVERT: A 37 LYS cc_start: 0.8618 (ttmt) cc_final: 0.7436 (tptp) REVERT: B 37 LYS cc_start: 0.8686 (ttmt) cc_final: 0.7574 (tptt) REVERT: B 53 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7463 (mm-30) REVERT: E 37 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8144 (tptp) outliers start: 31 outliers final: 26 residues processed: 325 average time/residue: 0.2195 time to fit residues: 103.8272 Evaluate side-chains 326 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN H 63 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.078615 restraints weight = 21705.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.080906 restraints weight = 11050.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.082446 restraints weight = 6846.728| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 12440 Z= 0.200 Angle : 0.730 59.192 16940 Z= 0.416 Chirality : 0.034 0.174 1940 Planarity : 0.003 0.043 2220 Dihedral : 3.490 15.052 1680 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.08 % Allowed : 25.38 % Favored : 72.54 % Cbeta Deviations : 0.07 % 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: 3.67 (0.21), residues: 1520 helix: 2.85 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.004 0.001 PHE N 16 TYR 0.009 0.001 TYR D 47 ARG 0.002 0.000 ARG J 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.17 seconds wall clock time: 47 minutes 38.79 seconds (2858.79 seconds total)